diff --git a/internal/storage/sqlite/ids.go b/internal/storage/sqlite/ids.go
index 97644aea..774c6a96 100644
--- a/internal/storage/sqlite/ids.go
+++ b/internal/storage/sqlite/ids.go
@@ -73,6 +73,38 @@ func isValidHex(s string) bool {
 	return true
 }
 
+// IsHierarchicalID checks if an issue ID is hierarchical (has a parent).
+// Hierarchical IDs have the format {parentID}.{N} where N is a numeric child suffix.
+// Returns true and the parent ID if hierarchical, false and empty string otherwise.
+//
+// This correctly handles prefixes that contain dots (e.g., "my.project-abc123"
+// is NOT hierarchical, but "my.project-abc123.1" IS hierarchical with parent
+// "my.project-abc123").
+//
+// The key insight is that hierarchical IDs always end with .{digits} where
+// the digits represent the child number (1, 2, 3, etc.).
+func IsHierarchicalID(id string) (isHierarchical bool, parentID string) {
+	lastDot := strings.LastIndex(id, ".")
+	if lastDot == -1 {
+		return false, ""
+	}
+
+	// Check if the suffix after the last dot is purely numeric
+	suffix := id[lastDot+1:]
+	if len(suffix) == 0 {
+		return false, ""
+	}
+
+	for _, c := range suffix {
+		if c < '0' || c > '9' {
+			return false, ""
+		}
+	}
+
+	// It's hierarchical - parent is everything before the last dot
+	return true, id[:lastDot]
+}
+
 // 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 {
@@ -203,11 +235,8 @@ func EnsureIDs(ctx context.Context, conn *sql.Conn, prefix string, issues []*typ
 			}
 			
 			// For hierarchical IDs (bd-a3f8e9.1), ensure parent exists
-			if strings.Contains(issues[i].ID, ".") {
-				// Extract parent ID (everything before the last dot)
-				lastDot := strings.LastIndex(issues[i].ID, ".")
-				parentID := issues[i].ID[:lastDot]
-				
+			// Use IsHierarchicalID to correctly handle prefixes with dots (GH#508)
+			if isHierarchical, parentID := IsHierarchicalID(issues[i].ID); isHierarchical {
 				var parentCount int
 				err := conn.QueryRowContext(ctx, `SELECT COUNT(*) FROM issues WHERE id = ?`, parentID).Scan(&parentCount)
 				if err != nil {
diff --git a/internal/storage/sqlite/ids_test.go b/internal/storage/sqlite/ids_test.go
new file mode 100644
index 00000000..2b954b99
--- /dev/null
+++ b/internal/storage/sqlite/ids_test.go
@@ -0,0 +1,134 @@
+package sqlite
+
+import "testing"
+
+// TestIsHierarchicalID tests the IsHierarchicalID function which detects
+// if an issue ID is hierarchical (has a parent) based on the .N suffix pattern.
+// This test covers the fix for GH#508 where prefixes with dots were incorrectly
+// flagged as hierarchical.
+func TestIsHierarchicalID(t *testing.T) {
+	tests := []struct {
+		name             string
+		id               string
+		wantHierarchical bool
+		wantParentID     string
+	}{
+		// Standard hierarchical IDs
+		{
+			name:             "simple child .1",
+			id:               "bd-abc123.1",
+			wantHierarchical: true,
+			wantParentID:     "bd-abc123",
+		},
+		{
+			name:             "child .2",
+			id:               "bd-xyz789.2",
+			wantHierarchical: true,
+			wantParentID:     "bd-xyz789",
+		},
+		{
+			name:             "multi-digit child .10",
+			id:               "bd-test.10",
+			wantHierarchical: true,
+			wantParentID:     "bd-test",
+		},
+		{
+			name:             "large child number .999",
+			id:               "bd-issue.999",
+			wantHierarchical: true,
+			wantParentID:     "bd-issue",
+		},
+		{
+			name:             "nested hierarchical",
+			id:               "bd-parent.1.2",
+			wantHierarchical: true,
+			wantParentID:     "bd-parent.1",
+		},
+
+		// Non-hierarchical IDs (no suffix or non-numeric suffix)
+		{
+			name:             "simple top-level",
+			id:               "bd-abc123",
+			wantHierarchical: false,
+			wantParentID:     "",
+		},
+		{
+			name:             "no dot at all",
+			id:               "test-issue",
+			wantHierarchical: false,
+			wantParentID:     "",
+		},
+
+		// GH#508: Prefixes with dots should NOT be detected as hierarchical
+		{
+			name:             "prefix with dot - my.project",
+			id:               "my.project-abc123",
+			wantHierarchical: false,
+			wantParentID:     "",
+		},
+		{
+			name:             "prefix with multiple dots",
+			id:               "com.example.app-issue1",
+			wantHierarchical: false,
+			wantParentID:     "",
+		},
+		{
+			name:             "prefix with dot AND hierarchical child",
+			id:               "my.project-abc123.1",
+			wantHierarchical: true,
+			wantParentID:     "my.project-abc123",
+		},
+		{
+			name:             "complex prefix with hierarchical",
+			id:               "com.example.app-xyz.5",
+			wantHierarchical: true,
+			wantParentID:     "com.example.app-xyz",
+		},
+
+		// Edge cases
+		{
+			name:             "dot but non-numeric suffix",
+			id:               "bd-abc.def",
+			wantHierarchical: false,
+			wantParentID:     "",
+		},
+		{
+			name:             "mixed suffix (starts with digit)",
+			id:               "bd-test.1abc",
+			wantHierarchical: false,
+			wantParentID:     "",
+		},
+		{
+			name:             "trailing dot only",
+			id:               "bd-test.",
+			wantHierarchical: false,
+			wantParentID:     "",
+		},
+		{
+			name:             "empty after dot",
+			id:               "bd-test.",
+			wantHierarchical: false,
+			wantParentID:     "",
+		},
+		{
+			name:             "child 0",
+			id:               "bd-parent.0",
+			wantHierarchical: true,
+			wantParentID:     "bd-parent",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			gotHierarchical, gotParentID := IsHierarchicalID(tt.id)
+			if gotHierarchical != tt.wantHierarchical {
+				t.Errorf("IsHierarchicalID(%q) hierarchical = %v, want %v",
+					tt.id, gotHierarchical, tt.wantHierarchical)
+			}
+			if gotParentID != tt.wantParentID {
+				t.Errorf("IsHierarchicalID(%q) parentID = %q, want %q",
+					tt.id, gotParentID, tt.wantParentID)
+			}
+		})
+	}
+}
diff --git a/internal/storage/sqlite/migrations/016_orphan_detection.go b/internal/storage/sqlite/migrations/016_orphan_detection.go
index d047f4a8..9319fd7a 100644
--- a/internal/storage/sqlite/migrations/016_orphan_detection.go
+++ b/internal/storage/sqlite/migrations/016_orphan_detection.go
@@ -7,23 +7,36 @@ import (
 )
 
 // MigrateOrphanDetection detects orphaned child issues and logs them for user action
-// Orphaned children are issues with hierarchical IDs (e.g., "parent.child") where the
+// Orphaned children are issues with hierarchical IDs (e.g., "parent.1") where the
 // parent issue no longer exists in the database.
 //
+// Hierarchical IDs have the format {parentID}.{N} where N is a numeric child suffix.
+// This correctly handles prefixes that contain dots (e.g., "my.project-abc123" is NOT
+// hierarchical, but "my.project-abc123.1" IS hierarchical). See GH#508.
+//
 // This migration does NOT automatically delete or convert orphans - it only logs them
 // so the user can decide whether to:
 // - Delete the orphans if they're no longer needed
 // - Convert them to top-level issues by renaming them
 // - Restore the missing parent issues
 func MigrateOrphanDetection(db *sql.DB) error {
-	// Query for orphaned children using the pattern from the issue description:
-	// SELECT id FROM issues WHERE id LIKE '%.%'
-	// AND substr(id, 1, instr(id || '.', '.') - 1) NOT IN (SELECT id FROM issues)
+	// Query for orphaned children:
+	// - Must end with .N where N is 1-4 digits (covers child numbers 0-9999)
+	// - Parent (everything before the last .N) must not exist in issues table
+	// - Uses GLOB patterns to ensure suffix is purely numeric
+	// - rtrim removes trailing digits, then trailing dot, to get parent ID
+	//
+	// GH#508: The old query used instr() to find the first dot, which incorrectly
+	// flagged IDs with dots in the prefix (e.g., "my.project-abc") as orphans.
+	// The fix uses GLOB patterns to only match IDs ending with .{digits}.
 	rows, err := db.Query(`
 		SELECT id
 		FROM issues
-		WHERE id LIKE '%.%'
-		  AND substr(id, 1, instr(id || '.', '.') - 1) NOT IN (SELECT id FROM issues)
+		WHERE
+		  -- Must end with .N where N is 1-4 digits (child number suffix)
+		  (id GLOB '*.[0-9]' OR id GLOB '*.[0-9][0-9]' OR id GLOB '*.[0-9][0-9][0-9]' OR id GLOB '*.[0-9][0-9][0-9][0-9]')
+		  -- Parent (remove trailing digits then dot) must not exist
+		  AND rtrim(rtrim(id, '0123456789'), '.') NOT IN (SELECT id FROM issues)
 		ORDER BY id
 	`)
 	if err != nil {
diff --git a/internal/storage/sqlite/migrations_test.go b/internal/storage/sqlite/migrations_test.go
index 2a621756..50be9801 100644
--- a/internal/storage/sqlite/migrations_test.go
+++ b/internal/storage/sqlite/migrations_test.go
@@ -620,4 +620,83 @@ func TestMigrateOrphanDetection(t *testing.T) {
 			}
 		}
 	})
+
+	// GH#508: Verify that prefixes with dots don't trigger false positives
+	t.Run("prefix with dots is not flagged as orphan", func(t *testing.T) {
+		store, cleanup := setupTestDB(t)
+		defer cleanup()
+		db := store.db
+
+		// Override the prefix for this test
+		_, err := db.Exec(`UPDATE config SET value = 'my.project' WHERE key = 'issue_prefix'`)
+		if err != nil {
+			t.Fatalf("failed to update prefix: %v", err)
+		}
+
+		// Insert issues with dotted prefix directly (bypassing prefix validation)
+		testCases := []struct {
+			id          string
+			expectOrphan bool
+		}{
+			// These should NOT be flagged as orphans (dots in prefix)
+			{"my.project-abc123", false},
+			{"my.project-xyz789", false},
+			{"com.example.app-issue1", false},
+
+			// This SHOULD be flagged as orphan (hierarchical, parent doesn't exist)
+			{"my.project-missing.1", true},
+		}
+
+		for _, tc := range testCases {
+			_, err := db.Exec(`
+				INSERT INTO issues (id, title, status, priority, issue_type, created_at, updated_at)
+				VALUES (?, ?, ?, ?, ?, datetime('now'), datetime('now'))
+			`, tc.id, "Test Issue", "open", 1, "task")
+			if err != nil {
+				t.Fatalf("failed to insert %s: %v", tc.id, err)
+			}
+		}
+
+		// Query for orphans using the same logic as the migration
+		rows, err := db.Query(`
+			SELECT id
+			FROM issues
+			WHERE
+			  (id GLOB '*.[0-9]' OR id GLOB '*.[0-9][0-9]' OR id GLOB '*.[0-9][0-9][0-9]' OR id GLOB '*.[0-9][0-9][0-9][0-9]')
+			  AND rtrim(rtrim(id, '0123456789'), '.') NOT IN (SELECT id FROM issues)
+			ORDER BY id
+		`)
+		if err != nil {
+			t.Fatalf("query failed: %v", err)
+		}
+		defer rows.Close()
+
+		var orphans []string
+		for rows.Next() {
+			var id string
+			if err := rows.Scan(&id); err != nil {
+				t.Fatalf("scan failed: %v", err)
+			}
+			orphans = append(orphans, id)
+		}
+
+		// Verify only the expected orphan is detected
+		if len(orphans) != 1 {
+			t.Errorf("expected 1 orphan, got %d: %v", len(orphans), orphans)
+		}
+		if len(orphans) == 1 && orphans[0] != "my.project-missing.1" {
+			t.Errorf("expected orphan 'my.project-missing.1', got %q", orphans[0])
+		}
+
+		// Verify non-hierarchical dotted IDs are NOT flagged
+		for _, tc := range testCases {
+			if !tc.expectOrphan {
+				for _, orphan := range orphans {
+					if orphan == tc.id {
+						t.Errorf("false positive: %s was incorrectly flagged as orphan", tc.id)
+					}
+				}
+			}
+		}
+	})
 }
diff --git a/internal/storage/sqlite/queries.go b/internal/storage/sqlite/queries.go
index 37e6330e..e8290b8e 100644
--- a/internal/storage/sqlite/queries.go
+++ b/internal/storage/sqlite/queries.go
@@ -122,7 +122,8 @@ func (s *SQLiteStorage) CreateIssue(ctx context.Context, issue *types.Issue, act
 		}
 
 		// For hierarchical IDs (bd-a3f8e9.1), ensure parent exists
-		if strings.Contains(issue.ID, ".") {
+		// Use IsHierarchicalID to correctly handle prefixes with dots (GH#508)
+		if isHierarchical, parentID := IsHierarchicalID(issue.ID); isHierarchical {
 			// Try to resurrect entire parent chain if any parents are missing
 			// Use the conn-based version to participate in the same transaction
 			resurrected, err := s.tryResurrectParentChainWithConn(ctx, conn, issue.ID)
@@ -131,8 +132,6 @@ func (s *SQLiteStorage) CreateIssue(ctx context.Context, issue *types.Issue, act
 			}
 			if !resurrected {
 				// Parent(s) not found in JSONL history - cannot proceed
-				lastDot := strings.LastIndex(issue.ID, ".")
-				parentID := issue.ID[:lastDot]
 				return fmt.Errorf("parent issue %s does not exist and could not be resurrected from JSONL history", parentID)
 			}
 		}
diff --git a/internal/storage/sqlite/transaction.go b/internal/storage/sqlite/transaction.go
index b143fbde..a8919074 100644
--- a/internal/storage/sqlite/transaction.go
+++ b/internal/storage/sqlite/transaction.go
@@ -137,7 +137,8 @@ func (t *sqliteTxStorage) CreateIssue(ctx context.Context, issue *types.Issue, a
 		}
 
 		// For hierarchical IDs (bd-a3f8e9.1), ensure parent exists
-		if strings.Contains(issue.ID, ".") {
+		// Use IsHierarchicalID to correctly handle prefixes with dots (GH#508)
+		if isHierarchical, parentID := IsHierarchicalID(issue.ID); isHierarchical {
 			// Try to resurrect entire parent chain if any parents are missing
 			resurrected, err := t.parent.tryResurrectParentChainWithConn(ctx, t.conn, issue.ID)
 			if err != nil {
@@ -145,8 +146,6 @@ func (t *sqliteTxStorage) CreateIssue(ctx context.Context, issue *types.Issue, a
 			}
 			if !resurrected {
 				// Parent(s) not found in JSONL history - cannot proceed
-				lastDot := strings.LastIndex(issue.ID, ".")
-				parentID := issue.ID[:lastDot]
 				return fmt.Errorf("parent issue %s does not exist and could not be resurrected from JSONL history", parentID)
 			}
 		}