diff --git a/internal/autoimport/autoimport.go b/internal/autoimport/autoimport.go
index 74d140e2..f82bf6bf 100644
--- a/internal/autoimport/autoimport.go
+++ b/internal/autoimport/autoimport.go
@@ -67,14 +67,7 @@ func AutoImportIfNewer(ctx context.Context, store storage.Storage, dbPath string
 
 	// Find JSONL using database directory (same logic as beads.FindJSONLPath)
 	dbDir := filepath.Dir(dbPath)
-	pattern := filepath.Join(dbDir, "*.jsonl")
-	matches, err := filepath.Glob(pattern)
-	var jsonlPath string
-	if err == nil && len(matches) > 0 {
-		jsonlPath = matches[0]
-	} else {
-		jsonlPath = filepath.Join(dbDir, "issues.jsonl")
-	}
+	jsonlPath := FindJSONLInDir(dbDir)
 	if jsonlPath == "" {
 		notify.Debugf("auto-import skipped, JSONL not found")
 		return nil
@@ -287,19 +280,7 @@ func CheckStaleness(ctx context.Context, store storage.Storage, dbPath string) (
 
 	// Find JSONL using database directory
 	dbDir := filepath.Dir(dbPath)
-	pattern := filepath.Join(dbDir, "*.jsonl")
-	matches, err := filepath.Glob(pattern)
-	if err != nil {
-		// Glob failed - this is abnormal
-		return false, fmt.Errorf("failed to find JSONL file: %w", err)
-	}
-
-	var jsonlPath string
-	if len(matches) > 0 {
-		jsonlPath = matches[0]
-	} else {
-		jsonlPath = filepath.Join(dbDir, "issues.jsonl")
-	}
+	jsonlPath := FindJSONLInDir(dbDir)
 
 	stat, err := os.Stat(jsonlPath)
 	if err != nil {
@@ -313,3 +294,47 @@ func CheckStaleness(ctx context.Context, store storage.Storage, dbPath string) (
 
 	return stat.ModTime().After(lastImportTime), nil
 }
+
+// FindJSONLInDir finds the JSONL file in the given directory.
+// It prefers issues.jsonl over other .jsonl files to prevent accidentally
+// reading/writing to deletions.jsonl or merge artifacts (bd-tqo fix).
+// Returns empty string if no suitable JSONL file is found.
+func FindJSONLInDir(dbDir string) string {
+	pattern := filepath.Join(dbDir, "*.jsonl")
+	matches, err := filepath.Glob(pattern)
+	if err != nil || len(matches) == 0 {
+		// Default to issues.jsonl if glob fails or no matches
+		return filepath.Join(dbDir, "issues.jsonl")
+	}
+
+	// Prefer issues.jsonl over other .jsonl files (bd-tqo fix)
+	// This prevents accidentally using deletions.jsonl or merge artifacts
+	for _, match := range matches {
+		if filepath.Base(match) == "issues.jsonl" {
+			return match
+		}
+	}
+
+	// Fall back to beads.jsonl for legacy support
+	for _, match := range matches {
+		if filepath.Base(match) == "beads.jsonl" {
+			return match
+		}
+	}
+
+	// Last resort: use first match (but skip deletions.jsonl and merge artifacts)
+	for _, match := range matches {
+		base := filepath.Base(match)
+		// Skip deletions manifest and merge artifacts
+		if base == "deletions.jsonl" ||
+			base == "beads.base.jsonl" ||
+			base == "beads.left.jsonl" ||
+			base == "beads.right.jsonl" {
+			continue
+		}
+		return match
+	}
+
+	// If only deletions/merge files exist, default to issues.jsonl
+	return filepath.Join(dbDir, "issues.jsonl")
+}
diff --git a/internal/autoimport/autoimport_test.go b/internal/autoimport/autoimport_test.go
index 70d02964..d1f42f88 100644
--- a/internal/autoimport/autoimport_test.go
+++ b/internal/autoimport/autoimport_test.go
@@ -517,3 +517,79 @@ func TestStderrNotifier(t *testing.T) {
 		notify.Infof("test info")
 	})
 }
+
+// TestFindJSONLInDir tests that FindJSONLInDir correctly prefers issues.jsonl
+// and avoids deletions.jsonl and merge artifacts (bd-tqo fix)
+func TestFindJSONLInDir(t *testing.T) {
+	tests := []struct {
+		name     string
+		files    []string
+		expected string
+	}{
+		{
+			name:     "only issues.jsonl",
+			files:    []string{"issues.jsonl"},
+			expected: "issues.jsonl",
+		},
+		{
+			name:     "issues.jsonl and deletions.jsonl - prefers issues",
+			files:    []string{"deletions.jsonl", "issues.jsonl"},
+			expected: "issues.jsonl",
+		},
+		{
+			name:     "issues.jsonl with merge artifacts - prefers issues",
+			files:    []string{"beads.base.jsonl", "beads.left.jsonl", "beads.right.jsonl", "issues.jsonl"},
+			expected: "issues.jsonl",
+		},
+		{
+			name:     "beads.jsonl as legacy fallback",
+			files:    []string{"beads.jsonl"},
+			expected: "beads.jsonl",
+		},
+		{
+			name:     "issues.jsonl preferred over beads.jsonl",
+			files:    []string{"beads.jsonl", "issues.jsonl"},
+			expected: "issues.jsonl",
+		},
+		{
+			name:     "only deletions.jsonl - returns default issues.jsonl",
+			files:    []string{"deletions.jsonl"},
+			expected: "issues.jsonl",
+		},
+		{
+			name:     "only merge artifacts - returns default issues.jsonl",
+			files:    []string{"beads.base.jsonl", "beads.left.jsonl", "beads.right.jsonl"},
+			expected: "issues.jsonl",
+		},
+		{
+			name:     "no files - returns default issues.jsonl",
+			files:    []string{},
+			expected: "issues.jsonl",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			tmpDir, err := os.MkdirTemp("", "bd-findjsonl-test-*")
+			if err != nil {
+				t.Fatal(err)
+			}
+			defer os.RemoveAll(tmpDir)
+
+			// Create test files
+			for _, file := range tt.files {
+				path := filepath.Join(tmpDir, file)
+				if err := os.WriteFile(path, []byte("{}"), 0644); err != nil {
+					t.Fatal(err)
+				}
+			}
+
+			result := FindJSONLInDir(tmpDir)
+			got := filepath.Base(result)
+
+			if got != tt.expected {
+				t.Errorf("FindJSONLInDir() = %q, want %q", got, tt.expected)
+			}
+		})
+	}
+}
diff --git a/internal/rpc/server_export_import_auto.go b/internal/rpc/server_export_import_auto.go
index c859937c..1c7018d8 100644
--- a/internal/rpc/server_export_import_auto.go
+++ b/internal/rpc/server_export_import_auto.go
@@ -441,15 +441,9 @@ func hasUncommittedBeadsFiles(workspacePath string) bool {
 // CRITICAL: Must populate all issue data (deps, labels, comments) to prevent data loss
 func (s *Server) triggerExport(ctx context.Context, store storage.Storage, dbPath string) error {
 	// Find JSONL path using database directory
+	// Use FindJSONLInDir to prefer issues.jsonl over other .jsonl files (bd-tqo fix)
 	dbDir := filepath.Dir(dbPath)
-	pattern := filepath.Join(dbDir, "*.jsonl")
-	matches, err := filepath.Glob(pattern)
-	var jsonlPath string
-	if err == nil && len(matches) > 0 {
-		jsonlPath = matches[0]
-	} else {
-		jsonlPath = filepath.Join(dbDir, "issues.jsonl")
-	}
+	jsonlPath := autoimport.FindJSONLInDir(dbDir)
 
 	// Get all issues from storage
 	sqliteStore, ok := store.(*sqlite.SQLiteStorage)