diff --git a/cmd/bd/export.go b/cmd/bd/export.go
index 302e345a..439b7cf0 100644
--- a/cmd/bd/export.go
+++ b/cmd/bd/export.go
@@ -76,18 +76,20 @@ Output to stdout by default, or use -o flag for file output.`,
 
 		// Write JSONL
 		encoder := json.NewEncoder(out)
+		exportedIDs := make([]string, 0, len(issues))
 		for _, issue := range issues {
 			if err := encoder.Encode(issue); err != nil {
 				fmt.Fprintf(os.Stderr, "Error encoding issue %s: %v\n", issue.ID, err)
 				os.Exit(1)
 			}
+			exportedIDs = append(exportedIDs, issue.ID)
 		}
 
 		// Only clear dirty issues and auto-flush state if exporting to the default JSONL path
 		// This prevents clearing dirty flags when exporting to custom paths (e.g., bd export -o backup.jsonl)
 		if output == "" || output == findJSONLPath() {
-			// Clear dirty issues since we just exported to the canonical JSONL file
-			if err := store.ClearDirtyIssues(ctx); err != nil {
+			// Clear only the issues that were actually exported (fixes bd-52 race condition)
+			if err := store.ClearDirtyIssuesByID(ctx, exportedIDs); err != nil {
 				fmt.Fprintf(os.Stderr, "Warning: failed to clear dirty issues: %v\n", err)
 			}
 
diff --git a/cmd/bd/main.go b/cmd/bd/main.go
index 8a0cdf06..4b1c4308 100644
--- a/cmd/bd/main.go
+++ b/cmd/bd/main.go
@@ -516,8 +516,8 @@ func flushToJSONL() {
 		return
 	}
 
-	// Clear dirty issues after successful export
-	if err := store.ClearDirtyIssues(ctx); err != nil {
+	// Clear only the dirty issues that were actually exported (fixes bd-52 race condition)
+	if err := store.ClearDirtyIssuesByID(ctx, dirtyIDs); err != nil {
 		// Don't fail the whole flush for this, but warn
 		fmt.Fprintf(os.Stderr, "Warning: failed to clear dirty issues: %v\n", err)
 	}
diff --git a/internal/storage/sqlite/dirty.go b/internal/storage/sqlite/dirty.go
index 4f8e52ea..a612a89e 100644
--- a/internal/storage/sqlite/dirty.go
+++ b/internal/storage/sqlite/dirty.go
@@ -77,6 +77,9 @@ func (s *SQLiteStorage) GetDirtyIssues(ctx context.Context) ([]string, error) {
 
 // ClearDirtyIssues removes all entries from the dirty_issues table
 // This should be called after a successful JSONL export
+//
+// WARNING: This has a race condition (bd-52). Use ClearDirtyIssuesByID instead
+// to only clear specific issues that were actually exported.
 func (s *SQLiteStorage) ClearDirtyIssues(ctx context.Context) error {
 	_, err := s.db.ExecContext(ctx, `DELETE FROM dirty_issues`)
 	if err != nil {
@@ -85,6 +88,34 @@ func (s *SQLiteStorage) ClearDirtyIssues(ctx context.Context) error {
 	return nil
 }
 
+// ClearDirtyIssuesByID removes specific issue IDs from the dirty_issues table
+// This avoids race conditions by only clearing issues that were actually exported
+func (s *SQLiteStorage) ClearDirtyIssuesByID(ctx context.Context, issueIDs []string) error {
+	if len(issueIDs) == 0 {
+		return nil
+	}
+
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer tx.Rollback()
+
+	stmt, err := tx.PrepareContext(ctx, `DELETE FROM dirty_issues WHERE issue_id = ?`)
+	if err != nil {
+		return fmt.Errorf("failed to prepare statement: %w", err)
+	}
+	defer stmt.Close()
+
+	for _, issueID := range issueIDs {
+		if _, err := stmt.ExecContext(ctx, issueID); err != nil {
+			return fmt.Errorf("failed to clear dirty issue %s: %w", issueID, err)
+		}
+	}
+
+	return tx.Commit()
+}
+
 // GetDirtyIssueCount returns the count of dirty issues (for monitoring/debugging)
 func (s *SQLiteStorage) GetDirtyIssueCount(ctx context.Context) (int, error) {
 	var count int
diff --git a/internal/storage/storage.go b/internal/storage/storage.go
index 0aab6450..1b3b4c96 100644
--- a/internal/storage/storage.go
+++ b/internal/storage/storage.go
@@ -45,7 +45,8 @@ type Storage interface {
 
 	// Dirty tracking (for incremental JSONL export)
 	GetDirtyIssues(ctx context.Context) ([]string, error)
-	ClearDirtyIssues(ctx context.Context) error
+	ClearDirtyIssues(ctx context.Context) error // WARNING: Race condition (bd-52), use ClearDirtyIssuesByID
+	ClearDirtyIssuesByID(ctx context.Context, issueIDs []string) error
 
 	// Config
 	SetConfig(ctx context.Context, key, value string) error