diff --git a/cmd/bd/sync.go b/cmd/bd/sync.go
index 9f800b7d..669747c1 100644
--- a/cmd/bd/sync.go
+++ b/cmd/bd/sync.go
@@ -168,6 +168,11 @@ Use --merge to merge the sync branch back to main branch.`,
 		// leaving the JSONL in an inconsistent state across worktrees.
 		// Track if we already exported during pre-flight to avoid redundant export later.
 		alreadyExported := false
+
+		// GH#885/bd-3bhl: Track pending export for atomic sync.
+		// When using deferred export, we store the result here and finalize
+		// only after git commit succeeds. If commit fails, we rollback JSONL.
+		var pendingExportResult *ExportResult
 		if hasUncommitted, err := gitHasUncommittedBeadsChanges(ctx); err != nil {
 			fmt.Fprintf(os.Stderr, "Warning: failed to check for uncommitted changes: %v\n", err)
 		} else if hasUncommitted {
@@ -311,10 +316,16 @@ Use --merge to merge the sync branch back to main branch.`,
 					FatalError("%v", err)
 				}
 
+				// GH#885/bd-3bhl: Use deferred export for atomic sync.
+				// Metadata updates are deferred until after git commit succeeds.
+				// This prevents SQLite from "lying" about sync state if commit fails.
 				fmt.Println("→ Exporting pending changes to JSONL...")
-				if err := exportToJSONL(ctx, jsonlPath); err != nil {
+				exportResult, err := exportToJSONLDeferred(ctx, jsonlPath)
+				if err != nil {
 					FatalError("exporting: %v", err)
 				}
+				// Store result for finalization after commit
+				pendingExportResult = exportResult
 			}
 
 			// Capture left snapshot (pre-pull state) for 3-way merge
@@ -356,9 +367,21 @@ Use --merge to merge the sync branch back to main branch.`,
 				} else {
 					committed, err := commitToExternalBeadsRepo(ctx, beadsDir, message, !noPush)
 					if err != nil {
-						FatalError("%v", err)
+						// GH#885/bd-3bhl: Rollback JSONL on commit failure
+						fmt.Fprintf(os.Stderr, "\n⚠️  Git commit failed - rolling back JSONL to previous state...\n")
+						if rollbackErr := rollbackJSONLFromGit(ctx, jsonlPath); rollbackErr != nil {
+							fmt.Fprintf(os.Stderr, "Warning: failed to rollback JSONL: %v\n", rollbackErr)
+							fmt.Fprintf(os.Stderr, "  Manual recovery: git checkout HEAD -- %s\n", jsonlPath)
+						} else {
+							fmt.Fprintf(os.Stderr, "✓ JSONL rolled back to last committed state\n")
+						}
+						FatalErrorWithHint(fmt.Sprintf("%v", err),
+							"fix the git issue and run 'bd sync' again")
 					}
 					if committed {
+						// GH#885/bd-3bhl: Finalize export after successful commit
+						finalizeExport(ctx, pendingExportResult)
+						pendingExportResult = nil
 						if !noPush {
 							fmt.Println("✓ Committed and pushed to external beads repo")
 						} else {
@@ -368,6 +391,9 @@ Use --merge to merge the sync branch back to main branch.`,
 				}
 			} else {
 				fmt.Println("→ No changes to commit in external beads repo")
+				// GH#885/bd-3bhl: No commit needed, but still finalize export metadata
+				finalizeExport(ctx, pendingExportResult)
+				pendingExportResult = nil
 			}
 
 			if !noPull {
@@ -549,10 +575,22 @@ Use --merge to merge the sync branch back to main branch.`,
 				fmt.Printf("→ Committing changes to sync branch '%s'...\n", syncBranchName)
 				result, err := syncbranch.CommitToSyncBranch(ctx, repoRoot, syncBranchName, jsonlPath, !noPush)
 				if err != nil {
-					FatalError("committing to sync branch: %v", err)
+					// GH#885/bd-3bhl: Rollback JSONL on commit failure
+					fmt.Fprintf(os.Stderr, "\n⚠️  Git commit failed - rolling back JSONL to previous state...\n")
+					if rollbackErr := rollbackJSONLFromGit(ctx, jsonlPath); rollbackErr != nil {
+						fmt.Fprintf(os.Stderr, "Warning: failed to rollback JSONL: %v\n", rollbackErr)
+						fmt.Fprintf(os.Stderr, "  Manual recovery: git checkout HEAD -- %s\n", jsonlPath)
+					} else {
+						fmt.Fprintf(os.Stderr, "✓ JSONL rolled back to last committed state\n")
+					}
+					FatalErrorWithHint(fmt.Sprintf("committing to sync branch: %v", err),
+						"fix the git issue and run 'bd sync' again")
 				}
 				if result.Committed {
 					fmt.Printf("✓ Committed to %s\n", syncBranchName)
+					// GH#885/bd-3bhl: Finalize export after successful commit
+					finalizeExport(ctx, pendingExportResult)
+					pendingExportResult = nil
 					if result.Pushed {
 						fmt.Printf("✓ Pushed %s to remote\n", syncBranchName)
 						pushedViaSyncBranch = true
@@ -561,6 +599,9 @@ Use --merge to merge the sync branch back to main branch.`,
 					// GH#812: When useSyncBranch is true, we always attempt commit
 					// (bypassing gitHasBeadsChanges). Report when worktree has no changes.
 					fmt.Println("→ No changes to commit")
+					// No commit needed, but still finalize export metadata
+					finalizeExport(ctx, pendingExportResult)
+					pendingExportResult = nil
 				}
 			} else {
 				// Regular commit to current branch
@@ -571,11 +612,26 @@ Use --merge to merge the sync branch back to main branch.`,
 					fmt.Println("→ Committing changes to git...")
 				}
 				if err := gitCommitBeadsDir(ctx, message); err != nil {
-					FatalError("committing: %v", err)
+					// GH#885/bd-3bhl: Rollback JSONL on commit failure
+					fmt.Fprintf(os.Stderr, "\n⚠️  Git commit failed - rolling back JSONL to previous state...\n")
+					if rollbackErr := rollbackJSONLFromGit(ctx, jsonlPath); rollbackErr != nil {
+						fmt.Fprintf(os.Stderr, "Warning: failed to rollback JSONL: %v\n", rollbackErr)
+						fmt.Fprintf(os.Stderr, "  Manual recovery: git checkout HEAD -- %s\n", jsonlPath)
+					} else {
+						fmt.Fprintf(os.Stderr, "✓ JSONL rolled back to last committed state\n")
+					}
+					FatalErrorWithHint(fmt.Sprintf("committing: %v", err),
+						"fix the git issue and run 'bd sync' again")
 				}
+				// GH#885/bd-3bhl: Finalize export after successful commit
+				finalizeExport(ctx, pendingExportResult)
+				pendingExportResult = nil
 			}
 		} else {
 			fmt.Println("→ No changes to commit")
+			// GH#885/bd-3bhl: No commit needed, but still finalize export metadata
+			finalizeExport(ctx, pendingExportResult)
+			pendingExportResult = nil
 		}
 
 		// Step 3: Pull from remote
diff --git a/cmd/bd/sync_git.go b/cmd/bd/sync_git.go
index 124967ae..e2e68f0d 100644
--- a/cmd/bd/sync_git.go
+++ b/cmd/bd/sync_git.go
@@ -492,6 +492,27 @@ func parseGitStatusForBeadsChanges(statusOutput string) bool {
 	return false
 }
 
+// rollbackJSONLFromGit restores the JSONL file from git HEAD after a failed commit.
+// This is part of the sync atomicity fix (GH#885/bd-3bhl): when git commit fails
+// after export, we restore the JSONL to its previous state so the working
+// directory stays consistent with the last successful sync.
+func rollbackJSONLFromGit(ctx context.Context, jsonlPath string) error {
+	// Check if the file is tracked by git
+	cmd := exec.CommandContext(ctx, "git", "ls-files", "--error-unmatch", jsonlPath)
+	if err := cmd.Run(); err != nil {
+		// File not tracked - nothing to restore
+		return nil
+	}
+
+	// Restore from HEAD
+	restoreCmd := exec.CommandContext(ctx, "git", "checkout", "HEAD", "--", jsonlPath) //nolint:gosec // G204: jsonlPath from internal beads.FindBeadsDir()
+	output, err := restoreCmd.CombinedOutput()
+	if err != nil {
+		return fmt.Errorf("git checkout failed: %w\n%s", err, output)
+	}
+	return nil
+}
+
 // getDefaultBranch returns the default branch name (main or master) for origin remote
 // Checks remote HEAD first, then falls back to checking if main/master exist
 func getDefaultBranch(ctx context.Context) string {
diff --git a/internal/syncbranch/integrity.go b/internal/syncbranch/integrity.go
index d688a8fe..a00a7aec 100644
--- a/internal/syncbranch/integrity.go
+++ b/internal/syncbranch/integrity.go
@@ -79,7 +79,13 @@ func CheckForcePush(ctx context.Context, store storage.Storage, repoRoot, syncBr
 	status.Remote = getRemoteForBranch(ctx, worktreePath, syncBranch)
 
 	// Fetch from remote to get latest state
-	fetchCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "fetch", status.Remote, syncBranch) // #nosec G204 - repoRoot/syncBranch are validated git inputs
+	// bd-4hh5: Use explicit refspec to ensure the remote-tracking ref is always updated.
+	// Without an explicit refspec, `git fetch origin beads-sync` only updates
+	// refs/remotes/origin/beads-sync if it already exists. On fresh clones or
+	// after ref cleanup, this can leave the tracking ref stale, causing
+	// false-positive force-push detection when comparing against wrong commits.
+	refspec := fmt.Sprintf("+refs/heads/%s:refs/remotes/%s/%s", syncBranch, status.Remote, syncBranch)
+	fetchCmd := exec.CommandContext(ctx, "git", "-C", repoRoot, "fetch", status.Remote, refspec) // #nosec G204 - repoRoot/syncBranch are validated git inputs
 	fetchOutput, err := fetchCmd.CombinedOutput()
 	if err != nil {
 		// Check if remote branch doesn't exist