diff --git a/internal/storage/sqlite/batch_ops.go b/internal/storage/sqlite/batch_ops.go
index 1d8df816..87baed0d 100644
--- a/internal/storage/sqlite/batch_ops.go
+++ b/internal/storage/sqlite/batch_ops.go
@@ -102,6 +102,30 @@ func bulkMarkDirty(ctx context.Context, conn *sql.Conn, issues []*types.Issue) e
 	return markDirtyBatch(ctx, conn, issues)
 }
 
+// updateChildCountersForHierarchicalIDs updates child_counters for all hierarchical IDs in the batch.
+// This is called AFTER issues are inserted so that parents exist for the foreign key constraint.
+// (GH#728 fix)
+func updateChildCountersForHierarchicalIDs(ctx context.Context, conn *sql.Conn, issues []*types.Issue) error {
+	for _, issue := range issues {
+		if issue.ID == "" {
+			continue // Skip issues that were filtered out (e.g., OrphanSkip)
+		}
+		if parentID, childNum, ok := ParseHierarchicalID(issue.ID); ok {
+			// Only update if parent exists (it should after insert, but check to be safe)
+			var parentCount int
+			if err := conn.QueryRowContext(ctx, `SELECT COUNT(*) FROM issues WHERE id = ?`, parentID).Scan(&parentCount); err != nil {
+				return fmt.Errorf("failed to check parent existence for %s: %w", parentID, err)
+			}
+			if parentCount > 0 {
+				if err := ensureChildCounterUpdatedWithConn(ctx, conn, parentID, childNum); err != nil {
+					return err
+				}
+			}
+		}
+	}
+	return nil
+}
+
 // checkForExistingIDs verifies that:
 // 1. There are no duplicate IDs within the batch itself
 // 2. None of the issue IDs already exist in the database
@@ -271,6 +295,12 @@ func (s *SQLiteStorage) CreateIssuesWithFullOptions(ctx context.Context, issues
 		return wrapDBError("bulk insert issues", err)
 	}
 
+	// Phase 4.5: Update child counters for hierarchical IDs (GH#728 fix)
+	// This must happen AFTER insert so parents exist for the foreign key constraint
+	if err := updateChildCountersForHierarchicalIDs(ctx, conn, issues); err != nil {
+		return wrapDBError("update child counters", err)
+	}
+
 	// Phase 5: Record creation events
 	if err := bulkRecordEvents(ctx, conn, issues, actor); err != nil {
 		return wrapDBError("record creation events", err)
diff --git a/internal/storage/sqlite/child_counters_test.go b/internal/storage/sqlite/child_counters_test.go
index 1a25c357..5916ffbd 100644
--- a/internal/storage/sqlite/child_counters_test.go
+++ b/internal/storage/sqlite/child_counters_test.go
@@ -78,11 +78,11 @@ func TestGetNextChildNumber(t *testing.T) {
 func TestGetNextChildNumber_DifferentParents(t *testing.T) {
 	store, cleanup := setupTestDB(t)
 	defer cleanup()
-	
+
 	ctx := context.Background()
 	parent1 := "bd-af78e9a2"
-	parent2 := "bd-af78e9a2.1"
-	
+	parent2 := "bd-bf89e0b3" // Use non-hierarchical ID to avoid counter interaction
+
 	// Create parent issues first
 	for _, id := range []string{parent1, parent2} {
 		parent := &types.Issue{
@@ -97,7 +97,7 @@ func TestGetNextChildNumber_DifferentParents(t *testing.T) {
 			t.Fatalf("failed to create parent issue %s: %v", id, err)
 		}
 	}
-	
+
 	// Each parent should have independent counters
 	child1_1, err := store.getNextChildNumber(ctx, parent1)
 	if err != nil {
@@ -106,7 +106,7 @@ func TestGetNextChildNumber_DifferentParents(t *testing.T) {
 	if child1_1 != 1 {
 		t.Errorf("expected parent1 child to be 1, got %d", child1_1)
 	}
-	
+
 	child2_1, err := store.getNextChildNumber(ctx, parent2)
 	if err != nil {
 		t.Fatalf("getNextChildNumber failed: %v", err)
@@ -114,7 +114,7 @@ func TestGetNextChildNumber_DifferentParents(t *testing.T) {
 	if child2_1 != 1 {
 		t.Errorf("expected parent2 child to be 1, got %d", child2_1)
 	}
-	
+
 	child1_2, err := store.getNextChildNumber(ctx, parent1)
 	if err != nil {
 		t.Fatalf("getNextChildNumber failed: %v", err)
@@ -186,10 +186,12 @@ func TestGetNextChildNumber_Concurrent(t *testing.T) {
 func TestGetNextChildNumber_NestedHierarchy(t *testing.T) {
 	store, cleanup := setupTestDB(t)
 	defer cleanup()
-	
+
 	ctx := context.Background()
-	
+
 	// Create parent issues for nested hierarchy
+	// Note: When creating bd-af78e9a2.1, the counter for bd-af78e9a2 is set to 1 (GH#728 fix)
+	// When creating bd-af78e9a2.1.2, the counter for bd-af78e9a2.1 is set to 2 (GH#728 fix)
 	parents := []string{"bd-af78e9a2", "bd-af78e9a2.1", "bd-af78e9a2.1.2"}
 	for _, id := range parents {
 		parent := &types.Issue{
@@ -204,21 +206,21 @@ func TestGetNextChildNumber_NestedHierarchy(t *testing.T) {
 			t.Fatalf("failed to create parent issue %s: %v", id, err)
 		}
 	}
-	
-	// Create nested hierarchy counters
-	// bd-af78e9a2 → .1, .2
-	// bd-af78e9a2.1 → .1.1, .1.2
-	// bd-af78e9a2.1.2 → .1.2.1, .1.2.2
-	
+
+	// With GH#728 fix, counters are updated when explicit hierarchical IDs are created:
+	// - Creating bd-af78e9a2.1 sets counter for bd-af78e9a2 to 1
+	// - Creating bd-af78e9a2.1.2 sets counter for bd-af78e9a2.1 to 2
+	// So getNextChildNumber returns the NEXT number after the existing children
+
 	tests := []struct {
 		parent   string
 		expected []int
 	}{
-		{"bd-af78e9a2", []int{1, 2}},
-		{"bd-af78e9a2.1", []int{1, 2}},
-		{"bd-af78e9a2.1.2", []int{1, 2}},
+		{"bd-af78e9a2", []int{2, 3}},     // counter was 1 after creating .1
+		{"bd-af78e9a2.1", []int{3, 4}},   // counter was 2 after creating .1.2
+		{"bd-af78e9a2.1.2", []int{1, 2}}, // no children created, starts at 1
 	}
-	
+
 	for _, tt := range tests {
 		for _, want := range tt.expected {
 			got, err := store.getNextChildNumber(ctx, tt.parent)
diff --git a/internal/storage/sqlite/child_id_test.go b/internal/storage/sqlite/child_id_test.go
index e2c9ffb5..b8335099 100644
--- a/internal/storage/sqlite/child_id_test.go
+++ b/internal/storage/sqlite/child_id_test.go
@@ -179,6 +179,80 @@ func TestCreateIssue_HierarchicalID(t *testing.T) {
 	}
 }
 
+// TestExplicitChildIDUpdatesCounter verifies that creating issues with explicit
+// hierarchical IDs (e.g., bd-test.1, bd-test.2) updates the child counter so that
+// GetNextChildID returns the correct next ID (GH#728 fix)
+func TestExplicitChildIDUpdatesCounter(t *testing.T) {
+	tmpFile := t.TempDir() + "/test.db"
+	defer os.Remove(tmpFile)
+	store := newTestStore(t, tmpFile)
+	defer store.Close()
+	ctx := context.Background()
+
+	// Create parent
+	parent := &types.Issue{
+		ID:          "bd-test",
+		Title:       "Parent",
+		Description: "Test parent",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeEpic,
+	}
+	if err := store.CreateIssue(ctx, parent, "test"); err != nil {
+		t.Fatalf("failed to create parent: %v", err)
+	}
+
+	// Create explicit child .1
+	child1 := &types.Issue{
+		ID:          "bd-test.1",
+		Title:       "Existing child 1",
+		Description: "Created with explicit ID",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+	if err := store.CreateIssue(ctx, child1, "test"); err != nil {
+		t.Fatalf("failed to create child1: %v", err)
+	}
+
+	// Create explicit child .2
+	child2 := &types.Issue{
+		ID:          "bd-test.2",
+		Title:       "Existing child 2",
+		Description: "Created with explicit ID",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+	if err := store.CreateIssue(ctx, child2, "test"); err != nil {
+		t.Fatalf("failed to create child2: %v", err)
+	}
+
+	// Now use GetNextChildID - should return .3 (not .1 which would collide)
+	nextID, err := store.GetNextChildID(ctx, "bd-test")
+	if err != nil {
+		t.Fatalf("GetNextChildID failed: %v", err)
+	}
+
+	expected := "bd-test.3"
+	if nextID != expected {
+		t.Errorf("GetNextChildID returned %s, expected %s (GH#728 - counter should be updated when explicit child IDs are created)", nextID, expected)
+	}
+
+	// Verify we can create an issue with the returned ID without collision
+	child3 := &types.Issue{
+		ID:          nextID,
+		Title:       "New child via --parent",
+		Description: "Created with GetNextChildID",
+		Status:      types.StatusOpen,
+		Priority:    2,
+		IssueType:   types.TypeTask,
+	}
+	if err := store.CreateIssue(ctx, child3, "test"); err != nil {
+		t.Fatalf("failed to create child3 with ID %s: %v", nextID, err)
+	}
+}
+
 func TestCreateIssue_HierarchicalID_ParentNotExists(t *testing.T) {
 	tmpFile := t.TempDir() + "/test.db"
 	defer os.Remove(tmpFile)
diff --git a/internal/storage/sqlite/hash_ids.go b/internal/storage/sqlite/hash_ids.go
index 90db2dc6..e5890c63 100644
--- a/internal/storage/sqlite/hash_ids.go
+++ b/internal/storage/sqlite/hash_ids.go
@@ -2,6 +2,7 @@ package sqlite
 
 import (
 	"context"
+	"database/sql"
 	"fmt"
 	"strings"
 )
@@ -65,4 +66,36 @@ func (s *SQLiteStorage) GetNextChildID(ctx context.Context, parentID string) (st
 	return childID, nil
 }
 
+// ensureChildCounterUpdated ensures the child_counters table has a value for parentID
+// that is at least childNum. This prevents ID collisions when children are created
+// with explicit IDs (via --id flag or import) rather than GetNextChildID.
+// (GH#728 fix)
+func (s *SQLiteStorage) ensureChildCounterUpdated(ctx context.Context, parentID string, childNum int) error {
+	_, err := s.db.ExecContext(ctx, `
+		INSERT INTO child_counters (parent_id, last_child)
+		VALUES (?, ?)
+		ON CONFLICT(parent_id) DO UPDATE SET
+			last_child = MAX(last_child, excluded.last_child)
+	`, parentID, childNum)
+	if err != nil {
+		return fmt.Errorf("failed to update child counter for parent %s: %w", parentID, err)
+	}
+	return nil
+}
+
+// ensureChildCounterUpdatedWithConn is like ensureChildCounterUpdated but uses a specific
+// connection for transaction consistency. (GH#728 fix)
+func ensureChildCounterUpdatedWithConn(ctx context.Context, conn *sql.Conn, parentID string, childNum int) error {
+	_, err := conn.ExecContext(ctx, `
+		INSERT INTO child_counters (parent_id, last_child)
+		VALUES (?, ?)
+		ON CONFLICT(parent_id) DO UPDATE SET
+			last_child = MAX(last_child, excluded.last_child)
+	`, parentID, childNum)
+	if err != nil {
+		return fmt.Errorf("failed to update child counter for parent %s: %w", parentID, err)
+	}
+	return nil
+}
+
 // generateHashID moved to ids.go (bd-0702)
diff --git a/internal/storage/sqlite/ids.go b/internal/storage/sqlite/ids.go
index 24da0619..e54b7f65 100644
--- a/internal/storage/sqlite/ids.go
+++ b/internal/storage/sqlite/ids.go
@@ -63,6 +63,33 @@ func IsHierarchicalID(id string) (isHierarchical bool, parentID string) {
 	return true, id[:lastDot]
 }
 
+// ParseHierarchicalID extracts the parent ID and child number from a hierarchical ID.
+// Returns (parentID, childNum, true) for hierarchical IDs like "bd-abc.1" -> ("bd-abc", 1, true).
+// Returns ("", 0, false) for non-hierarchical IDs.
+// (GH#728 fix)
+func ParseHierarchicalID(id string) (parentID string, childNum int, ok bool) {
+	lastDot := strings.LastIndex(id, ".")
+	if lastDot == -1 {
+		return "", 0, false
+	}
+
+	suffix := id[lastDot+1:]
+	if len(suffix) == 0 {
+		return "", 0, false
+	}
+
+	// Parse the numeric suffix
+	num := 0
+	for _, c := range suffix {
+		if c < '0' || c > '9' {
+			return "", 0, false
+		}
+		num = num*10 + int(c-'0')
+	}
+
+	return id[:lastDot], num, true
+}
+
 // ValidateIssueIDPrefix validates that an issue ID matches the configured prefix
 // Supports both top-level (bd-a3f8e9) and hierarchical (bd-a3f8e9.1) IDs
 func ValidateIssueIDPrefix(id, prefix string) error {
@@ -235,6 +262,18 @@ func EnsureIDs(ctx context.Context, conn *sql.Conn, prefix string, issues []*typ
 						// Default to allow for backward compatibility
 					}
 				}
+
+				// Update child_counters to prevent future ID collisions (GH#728 fix)
+				// When explicit child IDs are imported, the counter must be at least the child number
+				// Only update if parent exists (parentCount > 0) - for orphan modes, skip this
+				// The counter will be updated when the parent is actually created/exists
+				if parentCount > 0 {
+					if _, childNum, ok := ParseHierarchicalID(issues[i].ID); ok {
+						if err := ensureChildCounterUpdatedWithConn(ctx, conn, parentID, childNum); err != nil {
+							return fmt.Errorf("failed to update child counter: %w", err)
+						}
+					}
+				}
 			}
 
 			usedIDs[issues[i].ID] = true
diff --git a/internal/storage/sqlite/queries.go b/internal/storage/sqlite/queries.go
index 6ab807f0..a0e251ce 100644
--- a/internal/storage/sqlite/queries.go
+++ b/internal/storage/sqlite/queries.go
@@ -190,6 +190,14 @@ func (s *SQLiteStorage) CreateIssue(ctx context.Context, issue *types.Issue, act
 				// Parent(s) not found in JSONL history - cannot proceed
 				return fmt.Errorf("parent issue %s does not exist and could not be resurrected from JSONL history", parentID)
 			}
+
+			// Update child_counters to prevent future ID collisions (GH#728 fix)
+			// When explicit child IDs are used, the counter must be at least the child number
+			if _, childNum, ok := ParseHierarchicalID(issue.ID); ok {
+				if err := ensureChildCounterUpdatedWithConn(ctx, conn, parentID, childNum); err != nil {
+					return fmt.Errorf("failed to update child counter: %w", err)
+				}
+			}
 		}
 	}