fix: Post-PR #8 critical improvements (bd-64, bd-65, bd-66, bd-67)

This commit addresses all critical follow-up issues identified in the
code review of PR #8 (atomic counter implementation).

## bd-64: Fix SyncAllCounters performance bottleneck (P0)
- Replace SyncAllCounters() on every CreateIssue with lazy initialization
- Add ensureCounterInitialized() that only scans prefix-specific issues on first use
- Performance improvement: O(n) full table scan → O(1) for subsequent creates
- Add comprehensive tests in lazy_init_test.go

## bd-65: Add migration for issue_counters table (P1)
- Add migrateIssueCountersTable() similar to migrateDirtyIssuesTable()
- Checks if table is empty and syncs from existing issues on first open
- Handles both fresh databases and migrations from old databases
- Add comprehensive tests in migration_test.go (3 scenarios)

## bd-66: Make import counter sync failure fatal (P1)
- Change SyncAllCounters() failure from warning to fatal error in import
- Prevents ID collisions when counter sync fails
- Data integrity > convenience

## bd-67: Update test comments (P2)
- Update TestMultiProcessIDGeneration comments to reflect fix is in place
- Change "With the bug, we expect errors" → "After the fix, all should succeed"

All tests pass. Atomic counter implementation is now production-ready.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

cmd/bd/import.go

@@ -240,9 +240,11 @@ Behavior:
 
 		// Phase 5: Sync ID counters after importing issues with explicit IDs
 		// This prevents ID collisions with subsequently auto-generated issues
+		// CRITICAL: If this fails, subsequent auto-generated IDs WILL collide with imported issues
 		if err := sqliteStore.SyncAllCounters(ctx); err != nil {
-			fmt.Fprintf(os.Stderr, "Warning: failed to sync ID counters: %v\n", err)
+			fmt.Fprintf(os.Stderr, "Error: failed to sync ID counters: %v\n", err)
-			// Don't exit - this is not fatal, just a warning
+			fmt.Fprintf(os.Stderr, "Cannot proceed - auto-generated IDs would collide with imported issues.\n")
+			os.Exit(1)
 		}
 
 		// Phase 6: Process dependencies

internal/storage/sqlite/lazy_init_test.go

@@ -0,0 +1,217 @@
+package sqlite
+
+import (
+	"context"
+	"os"
+	"path/filepath"
+	"testing"
+
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// TestLazyCounterInitialization verifies that counters are initialized lazily
+// on first use, not by scanning the entire database on every CreateIssue
+func TestLazyCounterInitialization(t *testing.T) {
+	// Create temporary directory
+	tmpDir, err := os.MkdirTemp("", "beads-lazy-init-test-*")
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	dbPath := filepath.Join(tmpDir, "test.db")
+
+	// Initialize database
+	store, err := New(dbPath)
+	if err != nil {
+		t.Fatalf("failed to create storage: %v", err)
+	}
+	defer store.Close()
+
+	ctx := context.Background()
+
+	// Create some issues with explicit IDs (simulating import)
+	existingIssues := []string{"bd-5", "bd-10", "bd-15"}
+	for _, id := range existingIssues {
+		issue := &types.Issue{
+			ID:        id,
+			Title:     "Existing issue",
+			Status:    types.StatusOpen,
+			Priority:  2,
+			IssueType: types.TypeTask,
+		}
+		err := store.CreateIssue(ctx, issue, "test-user")
+		if err != nil {
+			t.Fatalf("CreateIssue with explicit ID failed: %v", err)
+		}
+	}
+
+	// Verify no counter exists yet (lazy init hasn't happened)
+	var count int
+	err = store.db.QueryRow(`SELECT COUNT(*) FROM issue_counters WHERE prefix = 'bd'`).Scan(&count)
+	if err != nil {
+		t.Fatalf("Failed to query counters: %v", err)
+	}
+
+	if count != 0 {
+		t.Errorf("Expected no counter yet, but found %d", count)
+	}
+
+	// Now create an issue with auto-generated ID
+	// This should trigger lazy initialization
+	autoIssue := &types.Issue{
+		Title:     "Auto-generated ID",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+
+	err = store.CreateIssue(ctx, autoIssue, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue with auto ID failed: %v", err)
+	}
+
+	// Verify the ID is correct (should be bd-16, after bd-15)
+	if autoIssue.ID != "bd-16" {
+		t.Errorf("Expected bd-16, got %s", autoIssue.ID)
+	}
+
+	// Verify counter was initialized
+	var lastID int
+	err = store.db.QueryRow(`SELECT last_id FROM issue_counters WHERE prefix = 'bd'`).Scan(&lastID)
+	if err != nil {
+		t.Fatalf("Failed to query counter: %v", err)
+	}
+
+	if lastID != 16 {
+		t.Errorf("Expected counter at 16, got %d", lastID)
+	}
+
+	// Create another issue - should NOT re-scan, just increment
+	anotherIssue := &types.Issue{
+		Title:     "Another auto-generated ID",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+
+	err = store.CreateIssue(ctx, anotherIssue, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	if anotherIssue.ID != "bd-17" {
+		t.Errorf("Expected bd-17, got %s", anotherIssue.ID)
+	}
+}
+
+// TestLazyCounterInitializationMultiplePrefix tests lazy init with multiple prefixes
+func TestLazyCounterInitializationMultiplePrefix(t *testing.T) {
+	store, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Set a custom prefix
+	err := store.SetConfig(ctx, "issue_prefix", "custom")
+	if err != nil {
+		t.Fatalf("SetConfig failed: %v", err)
+	}
+
+	// Create issue with default prefix first
+	err = store.SetConfig(ctx, "issue_prefix", "bd")
+	if err != nil {
+		t.Fatalf("SetConfig failed: %v", err)
+	}
+
+	bdIssue := &types.Issue{
+		Title:     "BD issue",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+
+	err = store.CreateIssue(ctx, bdIssue, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	if bdIssue.ID != "bd-1" {
+		t.Errorf("Expected bd-1, got %s", bdIssue.ID)
+	}
+
+	// Now switch to custom prefix
+	err = store.SetConfig(ctx, "issue_prefix", "custom")
+	if err != nil {
+		t.Fatalf("SetConfig failed: %v", err)
+	}
+
+	customIssue := &types.Issue{
+		Title:     "Custom issue",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+
+	err = store.CreateIssue(ctx, customIssue, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	if customIssue.ID != "custom-1" {
+		t.Errorf("Expected custom-1, got %s", customIssue.ID)
+	}
+
+	// Verify both counters exist
+	var count int
+	err = store.db.QueryRow(`SELECT COUNT(*) FROM issue_counters`).Scan(&count)
+	if err != nil {
+		t.Fatalf("Failed to query counters: %v", err)
+	}
+
+	if count != 2 {
+		t.Errorf("Expected 2 counters, got %d", count)
+	}
+}
+
+// TestCounterInitializationFromExisting tests that the counter
+// correctly initializes from the max ID of existing issues
+func TestCounterInitializationFromExisting(t *testing.T) {
+	store, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+
+	// Create issues with explicit IDs, out of order
+	explicitIDs := []string{"bd-5", "bd-100", "bd-42", "bd-7"}
+	for _, id := range explicitIDs {
+		issue := &types.Issue{
+			ID:        id,
+			Title:     "Explicit ID",
+			Status:    types.StatusOpen,
+			Priority:  2,
+			IssueType: types.TypeTask,
+		}
+		err := store.CreateIssue(ctx, issue, "test-user")
+		if err != nil {
+			t.Fatalf("CreateIssue failed: %v", err)
+		}
+	}
+
+	// Now auto-generate - should start at 101 (max is bd-100)
+	autoIssue := &types.Issue{
+		Title:     "Auto ID",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+
+	err := store.CreateIssue(ctx, autoIssue, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	if autoIssue.ID != "bd-101" {
+		t.Errorf("Expected bd-101 (max was bd-100), got %s", autoIssue.ID)
+	}
+}

internal/storage/sqlite/migration_test.go

@@ -0,0 +1,285 @@
+package sqlite
+
+import (
+	"context"
+	"database/sql"
+	"os"
+	"path/filepath"
+	"testing"
+
+	_ "github.com/mattn/go-sqlite3"
+	"github.com/steveyegge/beads/internal/types"
+)
+
+// TestMigrateIssueCountersTable tests that the migration properly creates
+// the issue_counters table and syncs it from existing issues
+func TestMigrateIssueCountersTable(t *testing.T) {
+	// Create temporary directory
+	tmpDir, err := os.MkdirTemp("", "beads-migration-test-*")
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	dbPath := filepath.Join(tmpDir, "test.db")
+
+	// Step 1: Create database with old schema (no issue_counters table)
+	db, err := sql.Open("sqlite3", dbPath+"?_journal_mode=WAL&_foreign_keys=ON")
+	if err != nil {
+		t.Fatalf("failed to open database: %v", err)
+	}
+
+	// Create minimal schema (issues table only, no issue_counters)
+	_, err = db.Exec(`
+		CREATE TABLE IF NOT EXISTS issues (
+			id TEXT PRIMARY KEY,
+			title TEXT NOT NULL,
+			description TEXT NOT NULL DEFAULT '',
+			design TEXT NOT NULL DEFAULT '',
+			acceptance_criteria TEXT NOT NULL DEFAULT '',
+			notes TEXT NOT NULL DEFAULT '',
+			status TEXT NOT NULL DEFAULT 'open',
+			priority INTEGER NOT NULL DEFAULT 2,
+			issue_type TEXT NOT NULL DEFAULT 'task',
+			assignee TEXT,
+			estimated_minutes INTEGER,
+			created_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+			updated_at DATETIME NOT NULL DEFAULT CURRENT_TIMESTAMP,
+			closed_at DATETIME
+		);
+
+		CREATE TABLE IF NOT EXISTS config (
+			key TEXT PRIMARY KEY,
+			value TEXT NOT NULL
+		);
+	`)
+	if err != nil {
+		t.Fatalf("failed to create old schema: %v", err)
+	}
+
+	// Insert some existing issues with IDs
+	_, err = db.Exec(`
+		INSERT INTO issues (id, title, status, priority, issue_type)
+		VALUES
+			('bd-5', 'Issue 5', 'open', 2, 'task'),
+			('bd-10', 'Issue 10', 'open', 2, 'task'),
+			('bd-15', 'Issue 15', 'open', 2, 'task'),
+			('custom-3', 'Custom 3', 'open', 2, 'task'),
+			('custom-7', 'Custom 7', 'open', 2, 'task')
+	`)
+	if err != nil {
+		t.Fatalf("failed to insert test issues: %v", err)
+	}
+
+	// Verify issue_counters table doesn't exist yet
+	var tableName string
+	err = db.QueryRow(`
+		SELECT name FROM sqlite_master
+		WHERE type='table' AND name='issue_counters'
+	`).Scan(&tableName)
+	if err != sql.ErrNoRows {
+		t.Fatalf("Expected issue_counters table to not exist, but it does")
+	}
+
+	db.Close()
+
+	// Step 2: Open database with New() which should trigger migration
+	store, err := New(dbPath)
+	if err != nil {
+		t.Fatalf("failed to create storage (migration failed): %v", err)
+	}
+	defer store.Close()
+
+	// Step 3: Verify issue_counters table now exists
+	err = store.db.QueryRow(`
+		SELECT name FROM sqlite_master
+		WHERE type='table' AND name='issue_counters'
+	`).Scan(&tableName)
+	if err != nil {
+		t.Fatalf("Expected issue_counters table to exist after migration: %v", err)
+	}
+
+	// Step 4: Verify counters were synced correctly
+	ctx := context.Background()
+
+	// Check bd prefix counter (max is bd-15)
+	var bdCounter int
+	err = store.db.QueryRowContext(ctx,
+		`SELECT last_id FROM issue_counters WHERE prefix = 'bd'`).Scan(&bdCounter)
+	if err != nil {
+		t.Fatalf("Failed to query bd counter: %v", err)
+	}
+	if bdCounter != 15 {
+		t.Errorf("Expected bd counter to be 15, got %d", bdCounter)
+	}
+
+	// Check custom prefix counter (max is custom-7)
+	var customCounter int
+	err = store.db.QueryRowContext(ctx,
+		`SELECT last_id FROM issue_counters WHERE prefix = 'custom'`).Scan(&customCounter)
+	if err != nil {
+		t.Fatalf("Failed to query custom counter: %v", err)
+	}
+	if customCounter != 7 {
+		t.Errorf("Expected custom counter to be 7, got %d", customCounter)
+	}
+
+	// Step 5: Verify next auto-generated IDs are correct
+	// Set prefix to bd
+	err = store.SetConfig(ctx, "issue_prefix", "bd")
+	if err != nil {
+		t.Fatalf("Failed to set config: %v", err)
+	}
+
+	issue := &types.Issue{
+		Title:     "New issue",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+
+	err = store.CreateIssue(ctx, issue, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	// Should be bd-16 (after bd-15)
+	if issue.ID != "bd-16" {
+		t.Errorf("Expected bd-16, got %s", issue.ID)
+	}
+}
+
+// TestMigrateIssueCountersTableEmptyDB tests migration on a fresh database
+func TestMigrateIssueCountersTableEmptyDB(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "beads-migration-empty-*")
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	dbPath := filepath.Join(tmpDir, "test.db")
+
+	// Create a fresh database with New() - should create table with no issues
+	store, err := New(dbPath)
+	if err != nil {
+		t.Fatalf("failed to create storage: %v", err)
+	}
+	defer store.Close()
+
+	// Verify table exists
+	var tableName string
+	err = store.db.QueryRow(`
+		SELECT name FROM sqlite_master
+		WHERE type='table' AND name='issue_counters'
+	`).Scan(&tableName)
+	if err != nil {
+		t.Fatalf("Expected issue_counters table to exist: %v", err)
+	}
+
+	// Verify no counters exist (since no issues)
+	var count int
+	err = store.db.QueryRow(`SELECT COUNT(*) FROM issue_counters`).Scan(&count)
+	if err != nil {
+		t.Fatalf("Failed to query counters: %v", err)
+	}
+	if count != 0 {
+		t.Errorf("Expected 0 counters in empty DB, got %d", count)
+	}
+
+	// Create first issue - should work fine
+	ctx := context.Background()
+	issue := &types.Issue{
+		Title:     "First issue",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+
+	err = store.CreateIssue(ctx, issue, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	// Should be bd-1
+	if issue.ID != "bd-1" {
+		t.Errorf("Expected bd-1, got %s", issue.ID)
+	}
+}
+
+// TestMigrateIssueCountersTableIdempotent verifies that running migration
+// multiple times is safe and doesn't corrupt data
+func TestMigrateIssueCountersTableIdempotent(t *testing.T) {
+	tmpDir, err := os.MkdirTemp("", "beads-migration-idempotent-*")
+	if err != nil {
+		t.Fatalf("failed to create temp dir: %v", err)
+	}
+	defer os.RemoveAll(tmpDir)
+
+	dbPath := filepath.Join(tmpDir, "test.db")
+
+	// Create database and migrate
+	store1, err := New(dbPath)
+	if err != nil {
+		t.Fatalf("failed to create storage: %v", err)
+	}
+
+	// Create some issues
+	ctx := context.Background()
+	issue := &types.Issue{
+		Title:     "Test issue",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+	err = store1.CreateIssue(ctx, issue, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	firstID := issue.ID // Should be bd-1
+	store1.Close()
+
+	// Re-open database (triggers migration again)
+	store2, err := New(dbPath)
+	if err != nil {
+		t.Fatalf("failed to re-open storage: %v", err)
+	}
+	defer store2.Close()
+
+	// Verify counter is still correct
+	var bdCounter int
+	err = store2.db.QueryRowContext(ctx,
+		`SELECT last_id FROM issue_counters WHERE prefix = 'bd'`).Scan(&bdCounter)
+	if err != nil {
+		t.Fatalf("Failed to query bd counter: %v", err)
+	}
+	if bdCounter != 1 {
+		t.Errorf("Expected bd counter to be 1 after idempotent migration, got %d", bdCounter)
+	}
+
+	// Create another issue
+	issue2 := &types.Issue{
+		Title:     "Second issue",
+		Status:    types.StatusOpen,
+		Priority:  2,
+		IssueType: types.TypeTask,
+	}
+	err = store2.CreateIssue(ctx, issue2, "test-user")
+	if err != nil {
+		t.Fatalf("CreateIssue failed: %v", err)
+	}
+
+	// Should be bd-2 (not bd-1 again)
+	if issue2.ID != "bd-2" {
+		t.Errorf("Expected bd-2, got %s", issue2.ID)
+	}
+
+	// Verify first issue still exists
+	firstIssue, err := store2.GetIssue(ctx, firstID)
+	if err != nil {
+		t.Fatalf("Failed to get first issue: %v", err)
+	}
+	if firstIssue == nil {
+		t.Errorf("First issue was lost after re-opening database")
+	}
+}

internal/storage/sqlite/sqlite.go

@@ -50,6 +50,11 @@ func New(path string) (*SQLiteStorage, error) {
 		return nil, fmt.Errorf("failed to migrate dirty_issues table: %w", err)
 	}
 
+	// Migrate existing databases to add issue_counters table if missing
+	if err := migrateIssueCountersTable(db); err != nil {
+		return nil, fmt.Errorf("failed to migrate issue_counters table: %w", err)
+	}
+
 	return &SQLiteStorage{
 		db: db,
 	}, nil
@@ -90,6 +95,66 @@ func migrateDirtyIssuesTable(db *sql.DB) error {
 	return nil
 }
 
+// migrateIssueCountersTable checks if the issue_counters table needs initialization.
+// This ensures existing databases created before the atomic counter feature get migrated automatically.
+// The table may already exist (created by schema), but be empty - in that case we still need to sync.
+func migrateIssueCountersTable(db *sql.DB) error {
+	// Check if the table exists (it should, created by schema)
+	var tableName string
+	err := db.QueryRow(`
+		SELECT name FROM sqlite_master
+		WHERE type='table' AND name='issue_counters'
+	`).Scan(&tableName)
+
+	tableExists := err == nil
+
+	if !tableExists {
+		if err != sql.ErrNoRows {
+			return fmt.Errorf("failed to check for issue_counters table: %w", err)
+		}
+		// Table doesn't exist, create it (shouldn't happen with schema, but handle it)
+		_, err := db.Exec(`
+			CREATE TABLE issue_counters (
+				prefix TEXT PRIMARY KEY,
+				last_id INTEGER NOT NULL DEFAULT 0
+			)
+		`)
+		if err != nil {
+			return fmt.Errorf("failed to create issue_counters table: %w", err)
+		}
+	}
+
+	// Check if table is empty - if so, we need to sync from existing issues
+	var count int
+	err = db.QueryRow(`SELECT COUNT(*) FROM issue_counters`).Scan(&count)
+	if err != nil {
+		return fmt.Errorf("failed to count issue_counters: %w", err)
+	}
+
+	if count == 0 {
+		// Table is empty, sync counters from existing issues to prevent ID collisions
+		// This is safe to do during migration since it's a one-time operation
+		_, err = db.Exec(`
+			INSERT INTO issue_counters (prefix, last_id)
+			SELECT
+				substr(id, 1, instr(id, '-') - 1) as prefix,
+				MAX(CAST(substr(id, instr(id, '-') + 1) AS INTEGER)) as max_id
+			FROM issues
+			WHERE instr(id, '-') > 0
+			  AND substr(id, instr(id, '-') + 1) GLOB '[0-9]*'
+			GROUP BY prefix
+			ON CONFLICT(prefix) DO UPDATE SET
+				last_id = MAX(last_id, excluded.last_id)
+		`)
+		if err != nil {
+			return fmt.Errorf("failed to sync counters during migration: %w", err)
+		}
+	}
+
+	// Table exists and is initialized (either was already populated, or we just synced it)
+	return nil
+}
+
 // getNextIDForPrefix atomically generates the next ID for a given prefix
 // Uses the issue_counters table for atomic, cross-process ID generation
 func (s *SQLiteStorage) getNextIDForPrefix(ctx context.Context, prefix string) (int, error) {
@@ -107,6 +172,43 @@ func (s *SQLiteStorage) getNextIDForPrefix(ctx context.Context, prefix string) (
 	return nextID, nil
 }
 
+// ensureCounterInitialized checks if a counter exists for the given prefix,
+// and initializes it from existing issues if needed. This is lazy initialization
+// to avoid scanning the entire issues table on every CreateIssue call.
+func (s *SQLiteStorage) ensureCounterInitialized(ctx context.Context, prefix string) error {
+	// Check if counter already exists for this prefix
+	var exists int
+	err := s.db.QueryRowContext(ctx,
+		`SELECT 1 FROM issue_counters WHERE prefix = ?`, prefix).Scan(&exists)
+
+	if err == nil {
+		// Counter exists, we're good
+		return nil
+	}
+
+	if err != sql.ErrNoRows {
+		// Unexpected error
+		return fmt.Errorf("failed to check counter existence: %w", err)
+	}
+
+	// Counter doesn't exist, initialize it from existing issues with this prefix
+	_, err = s.db.ExecContext(ctx, `
+		INSERT INTO issue_counters (prefix, last_id)
+		SELECT ?, COALESCE(MAX(CAST(substr(id, LENGTH(?) + 2) AS INTEGER)), 0)
+		FROM issues
+		WHERE id LIKE ? || '-%'
+		  AND substr(id, LENGTH(?) + 2) GLOB '[0-9]*'
+		ON CONFLICT(prefix) DO UPDATE SET
+			last_id = MAX(last_id, excluded.last_id)
+	`, prefix, prefix, prefix, prefix)
+
+	if err != nil {
+		return fmt.Errorf("failed to initialize counter for prefix %s: %w", prefix, err)
+	}
+
+	return nil
+}
+
 // SyncAllCounters synchronizes all ID counters based on existing issues in the database
 // This scans all issues and updates counters to prevent ID collisions with auto-generated IDs
 func (s *SQLiteStorage) SyncAllCounters(ctx context.Context) error {
@@ -137,19 +239,18 @@ func (s *SQLiteStorage) CreateIssue(ctx context.Context, issue *types.Issue, act
 
 	// Generate ID if not set (using atomic counter table)
 	if issue.ID == "" {
-		// Sync all counters first to ensure we don't collide with existing issues
-		// This handles the case where the database was created before this fix
-		// or issues were imported without syncing counters
-		if err := s.SyncAllCounters(ctx); err != nil {
-			return fmt.Errorf("failed to sync counters: %w", err)
-		}
-
 		// Get prefix from config, default to "bd"
 		prefix, err := s.GetConfig(ctx, "issue_prefix")
 		if err != nil || prefix == "" {
 			prefix = "bd"
 		}
 
+		// Ensure counter is initialized for this prefix (lazy initialization)
+		// Only scans issues with this prefix on first use, not the entire table
+		if err := s.ensureCounterInitialized(ctx, prefix); err != nil {
+			return fmt.Errorf("failed to initialize counter: %w", err)
+		}
+
 		// Atomically get next ID from counter table
 		nextID, err := s.getNextIDForPrefix(ctx, prefix)
 		if err != nil {

internal/storage/sqlite/sqlite_test.go

@@ -460,9 +460,9 @@ func TestMultiProcessIDGeneration(t *testing.T) {
 		ids[res.id] = true
 	}
 
-	// With the bug, we expect UNIQUE constraint errors
+	// After the fix (atomic counter), all operations should succeed without errors
 	if len(errors) > 0 {
-		t.Logf("Got %d errors (expected with current implementation):", len(errors))
+		t.Errorf("Expected no errors with atomic counter fix, got %d:", len(errors))
 		for _, err := range errors {
 			t.Logf("  - %v", err)
 		}
@@ -470,13 +470,9 @@ func TestMultiProcessIDGeneration(t *testing.T) {
 
 	t.Logf("Successfully created %d unique issues out of %d attempts", len(ids), numProcesses)
 
-	// After the fix, all should succeed
+	// All issues should be created successfully with unique IDs
 	if len(ids) != numProcesses {
 		t.Errorf("Expected %d unique IDs, got %d", numProcesses, len(ids))
 	}
-
-	if len(errors) > 0 {
-		t.Errorf("Expected no errors, got %d", len(errors))
-	}
 }