diff --git a/cmd/bd/daemon_sync_branch.go b/cmd/bd/daemon_sync_branch.go
index a0b66d9d..aa9f4805 100644
--- a/cmd/bd/daemon_sync_branch.go
+++ b/cmd/bd/daemon_sync_branch.go
@@ -64,14 +64,24 @@ func syncBranchCommitAndPush(ctx context.Context, store storage.Storage, autoPus
 	}
 	
 	// Sync JSONL file to worktree
-	// Use hardcoded relative path since JSONL is always at .beads/beads.jsonl
-	jsonlRelPath := filepath.Join(".beads", "beads.jsonl")
+	// Get the actual JSONL path (could be issues.jsonl, beads.base.jsonl, etc.)
+	jsonlPath := findJSONLPath()
+	if jsonlPath == "" {
+		return false, fmt.Errorf("JSONL path not found")
+	}
+	
+	// Convert absolute path to relative path from repo root
+	jsonlRelPath, err := filepath.Rel(repoRoot, jsonlPath)
+	if err != nil {
+		return false, fmt.Errorf("failed to get relative JSONL path: %w", err)
+	}
+	
 	if err := wtMgr.SyncJSONLToWorktree(worktreePath, jsonlRelPath); err != nil {
 		return false, fmt.Errorf("failed to sync JSONL to worktree: %w", err)
 	}
 	
 	// Check for changes in worktree
-	worktreeJSONLPath := filepath.Join(worktreePath, ".beads", "beads.jsonl")
+	worktreeJSONLPath := filepath.Join(worktreePath, jsonlRelPath)
 	hasChanges, err := gitHasChangesInWorktree(ctx, worktreePath, worktreeJSONLPath)
 	if err != nil {
 		return false, fmt.Errorf("failed to check for changes in worktree: %w", err)
@@ -225,9 +235,21 @@ func syncBranchPull(ctx context.Context, store storage.Storage, log daemonLogger
 	
 	log.log("Pulled sync branch %s", syncBranch)
 	
+	// Get the actual JSONL path
+	jsonlPath := findJSONLPath()
+	if jsonlPath == "" {
+		return false, fmt.Errorf("JSONL path not found")
+	}
+	
+	// Convert to relative path
+	jsonlRelPath, err := filepath.Rel(repoRoot, jsonlPath)
+	if err != nil {
+		return false, fmt.Errorf("failed to get relative JSONL path: %w", err)
+	}
+	
 	// Copy JSONL back to main repo
-	worktreeJSONLPath := filepath.Join(worktreePath, ".beads", "beads.jsonl")
-	mainJSONLPath := filepath.Join(repoRoot, ".beads", "beads.jsonl")
+	worktreeJSONLPath := filepath.Join(worktreePath, jsonlRelPath)
+	mainJSONLPath := jsonlPath
 	
 	// Check if worktree JSONL exists
 	if _, err := os.Stat(worktreeJSONLPath); os.IsNotExist(err) {