To sync two folders without deleting files in the destination, use an update style synchronization rather than a mirror. The source supplies missing or changed files, while destination only files remain in place.
This is the right pattern when the destination is an archive, long term backup, or collection that contains valid files no longer present in the current source.
If you are beginning with a browser workflow, first review how to sync two folders without installing software, then use the comparison process for copying only changed files to identify what the update should include.
Update and Mirror Solve Different Problems
People often use the word sync for several behaviors.
A mirror asks:
How can I make the destination look like the source?
An update asks:
How can I add current source changes to the destination without removing destination extras?
Those questions produce different actions.
Why Destination Only Files Matter
Suppose Folder A is:
Laptop/Photos/Current/
and Folder B is:
Archive/Photos/
The archive contains pictures from 2023, 2024, 2025, and 2026. The laptop contains only current work.
A mirror could identify old archive files as destination only and schedule them for deletion.
An update plan can leave them untouched while copying new or changed files from the laptop.
If preservation is your priority, destination only should normally map to no action.
Step 1: Compare the Folder Pair
Select Folder A and Folder B in the Free Online File Sync tool and run a comparison.
Review at least these categories:
- Only in A
- Only in B
- A newer
- B newer
- Different contents
- Identical
The B only category deserves special attention because those are the files a mirror might remove.
Step 2: Choose Update Destination
Update Destination should copy qualifying missing or changed source files into B without treating every B only file as unwanted.
The official FreeFileSync desktop manual describes its Update variant as a backup mode that does not delete source deleted items from the backup side. The browser project follows the same broad safety concept but is independent software.
Step 3: Check Changed File Direction
Preserving destination only files does not answer every conflict.
If a path exists on both sides and Folder B appears newer, you need a policy.
For a strict source driven update, A may still overwrite B. For a cautious archive workflow, you may prefer to stop and inspect newer destination versions before replacing them.
That is why a custom action can be valuable for ambiguous categories.
Step 4: Preview the Planned Copies
A safe update preview should show no automatic removals for unrelated destination only files.
Example:
Folder A:
Invoices/2026/April.pdf
Invoices/2026/May.pdf
Folder B:
Invoices/2025/December.pdf
Invoices/2026/April.pdf
Plan:
- Preserve
2025/December.pdf - Compare
2026/April.pdf - Copy
2026/May.pdf
The archive grows without being forced to match the smaller source exactly.
Step 5: Consider Filters
Update workflows are often used for backups, and backups benefit from careful scope.
You may want to exclude:
- Temporary files
- Cache directories
- Build output
- Large disposable exports
- System generated thumbnails
Filters should be visible in the comparison result so you know which data was ignored.
When Update Is Safer Than Mirror
Prefer Update Destination when:
- The destination is a cumulative archive.
- You have intentionally deleted source files to save space but still want them in backup.
- Several devices feed data into the destination.
- You are uncertain whether destination only files are obsolete.
- You want a conservative first pass.
A mirror is better when the destination is supposed to be an exact representation of the source.
Update Is Not Version History
An update workflow preserves extra destination files, but that does not automatically make it a version control system.
If report.docx exists on both sides and the selected rule replaces the destination version, the previous destination content may still be lost.
If keeping revisions matters, use Keep Both, a versioned backup strategy, or another system designed for history.
Browser Safety Boundaries
Browser file writes require permissions. The page cannot continue updating folders after it is closed, and it cannot access protected locations simply because the user named them.
Use this workflow for visible, user approved operations.
For scheduled or continuous synchronization, installed software is the more appropriate category.
Conclusion
To sync two folders without deleting files in the destination, choose an update style workflow, preserve destination only entries, inspect newer destination files, and confirm the preview before writing.
Use Free Online File Sync and select Update Destination when your backup should grow without being forced into an exact mirror. If you do want exact source matching, read How to Mirror One Folder to Another Safely.