diff --git a/internal/storage/memory/memory.go b/internal/storage/memory/memory.go
index b73e3fe2..ccf53d3d 100644
--- a/internal/storage/memory/memory.go
+++ b/internal/storage/memory/memory.go
@@ -1313,14 +1313,6 @@ func (m *MemoryStorage) GetDirtyIssues(ctx context.Context) ([]string, error) {
 	return dirtyIDs, nil
 }
 
-func (m *MemoryStorage) ClearDirtyIssues(ctx context.Context) error {
-	m.mu.Lock()
-	defer m.mu.Unlock()
-
-	m.dirty = make(map[string]bool)
-	return nil
-}
-
 func (m *MemoryStorage) ClearDirtyIssuesByID(ctx context.Context, issueIDs []string) error {
 	m.mu.Lock()
 	defer m.mu.Unlock()
diff --git a/internal/storage/memory/memory_test.go b/internal/storage/memory/memory_test.go
index ecbe1063..b613656c 100644
--- a/internal/storage/memory/memory_test.go
+++ b/internal/storage/memory/memory_test.go
@@ -698,8 +698,8 @@ func TestDirtyTracking(t *testing.T) {
 	}
 
 	// Clear dirty
-	if err := store.ClearDirtyIssues(ctx); err != nil {
-		t.Fatalf("ClearDirtyIssues failed: %v", err)
+	if err := store.ClearDirtyIssuesByID(ctx, dirty); err != nil {
+		t.Fatalf("ClearDirtyIssuesByID failed: %v", err)
 	}
 
 	dirty, err = store.GetDirtyIssues(ctx)
diff --git a/internal/storage/sqlite/dirty.go b/internal/storage/sqlite/dirty.go
index b1414021..9eb5e0a0 100644
--- a/internal/storage/sqlite/dirty.go
+++ b/internal/storage/sqlite/dirty.go
@@ -95,19 +95,6 @@ func (s *SQLiteStorage) GetDirtyIssueHash(ctx context.Context, issueID string) (
 	return hash.String, nil
 }
 
-// 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 {
-		return fmt.Errorf("failed to clear dirty issues: %w", err)
-	}
-	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 {
diff --git a/internal/storage/sqlite/dirty_test.go b/internal/storage/sqlite/dirty_test.go
index fadc415a..d8863e56 100644
--- a/internal/storage/sqlite/dirty_test.go
+++ b/internal/storage/sqlite/dirty_test.go
@@ -39,9 +39,9 @@ func TestMarkIssueDirty(t *testing.T) {
 	}
 
 	// Clear dirty issues
-	err = store.ClearDirtyIssues(ctx)
+	err = store.ClearDirtyIssuesByID(ctx, []string{issue.ID})
 	if err != nil {
-		t.Fatalf("ClearDirtyIssues failed: %v", err)
+		t.Fatalf("ClearDirtyIssuesByID failed: %v", err)
 	}
 
 	// Verify cleared
@@ -92,9 +92,9 @@ func TestMarkIssuesDirty(t *testing.T) {
 	}
 
 	// Clear all dirty issues
-	err := store.ClearDirtyIssues(ctx)
+	err := store.ClearDirtyIssuesByID(ctx, issueIDs)
 	if err != nil {
-		t.Fatalf("ClearDirtyIssues failed: %v", err)
+		t.Fatalf("ClearDirtyIssuesByID failed: %v", err)
 	}
 
 	// Mark multiple issues dirty at once
diff --git a/internal/storage/sqlite/events_test.go b/internal/storage/sqlite/events_test.go
index af772b90..cda9f273 100644
--- a/internal/storage/sqlite/events_test.go
+++ b/internal/storage/sqlite/events_test.go
@@ -212,9 +212,9 @@ func TestAddCommentMarksDirty(t *testing.T) {
 	}
 
 	// Clear dirty issues
-	err = store.ClearDirtyIssues(ctx)
+	err = store.ClearDirtyIssuesByID(ctx, []string{issue.ID})
 	if err != nil {
-		t.Fatalf("ClearDirtyIssues failed: %v", err)
+		t.Fatalf("ClearDirtyIssuesByID failed: %v", err)
 	}
 
 	// Add comment - should mark issue dirty
diff --git a/internal/storage/sqlite/labels_test.go b/internal/storage/sqlite/labels_test.go
index 614192b3..1582377a 100644
--- a/internal/storage/sqlite/labels_test.go
+++ b/internal/storage/sqlite/labels_test.go
@@ -351,9 +351,9 @@ func TestLabelMarksDirty(t *testing.T) {
 	}
 
 	// Clear dirty issues
-	err = store.ClearDirtyIssues(ctx)
+	err = store.ClearDirtyIssuesByID(ctx, []string{issue.ID})
 	if err != nil {
-		t.Fatalf("ClearDirtyIssues failed: %v", err)
+		t.Fatalf("ClearDirtyIssuesByID failed: %v", err)
 	}
 
 	// Add label - should mark issue dirty
@@ -372,9 +372,9 @@ func TestLabelMarksDirty(t *testing.T) {
 	}
 
 	// Clear dirty again
-	err = store.ClearDirtyIssues(ctx)
+	err = store.ClearDirtyIssuesByID(ctx, []string{issue.ID})
 	if err != nil {
-		t.Fatalf("ClearDirtyIssues failed: %v", err)
+		t.Fatalf("ClearDirtyIssuesByID failed: %v", err)
 	}
 
 	// Remove label - should mark issue dirty
diff --git a/internal/storage/storage.go b/internal/storage/storage.go
index 5df227c9..a4ff736f 100644
--- a/internal/storage/storage.go
+++ b/internal/storage/storage.go
@@ -126,7 +126,6 @@ type Storage interface {
 	// Dirty tracking (for incremental JSONL export)
 	GetDirtyIssues(ctx context.Context) ([]string, error)
 	GetDirtyIssueHash(ctx context.Context, issueID string) (string, error) // For timestamp-only dedup (bd-164)
-	ClearDirtyIssues(ctx context.Context) error                            // WARNING: Race condition (bd-52), use ClearDirtyIssuesByID
 	ClearDirtyIssuesByID(ctx context.Context, issueIDs []string) error
 
 	// Export hash tracking (for timestamp-only dedup, bd-164)