Help! disappearing files and multiplying folders after using sync!


I use Obsidian on two different machines (Mac/Pc) + iPhone. I used to sync to my vault stored in Dropbox only, and that worked nicely on the pcs.

I then bought access to sync, set everything up on my Mac, and everything worked nicely. I used my Mac mostly, and the PC on occasions.

After a PC session, I opened Obsidian on my Mac, and noticed that a) files had dissapeared (can’t find a system in what has disappeared and not) and b) a folder within my vault had multiplied itself numerous times, looking like this in the file structure in Obsidian:


What have I done wrong? Should I have disconnected everything from the ‘original’ vault in Dropbox after syncing once?

And; is there a way to recover the files (can’t find them when I search in File Recovery/Snapshots either).

Things I have tried

Swearing. Didn’t work. Searching for files in Dropbox, and in File Recovery from inside Obsidian. Didn’t work.

What I’m trying to do

Ok, where do we start?
I am not sure if you were using also FolderSync/Dropsync for your phone andt this caused this inception effect.

First make a backup copy of whatever you have now.

Regarding recovery, you have 3 paths.

  1. Recovery using Dropbox 30day deleted files window on free account and infinite on pro accounts
  2. Obsidian Sync Versioning
  3. Obsidian File Recovery

Lastly, I advise against using obsidian sync and dropbox at the same time on the same files.

Hmmmm is there any chance you configured the Obsidian vaults to be in a parent folder on one of your devices when using Obsidian Sync, and then when Obsidian Sync tried to replicate the folder structure, Dropbox picked it up and synced it across, causing infinite recursion?

In general, we don’t encourage using two sync providers to sync the same set of files across the same set of devices. In that case, race conditions could cause file corruption, duplication, or worst case… well unknown issues like this one.

You can, however, still have a backup copy of your vault in Dropbox by only using Dropbox on your primary device (in this case, your mac) and have Obsidian Sync keeps everything in sync, so as to avoid the conflicts between two sync services.

More docs here: Obsidian Sync

As for file recovery, Dropbox should have a 30-day version history like WhiteNoise mentioned that should make it possible to recover any files that was deleted, but I suspect your files aren’t really deleted; they’re just completely shadowed by the weird folder structure that was generated when the two sync solution conflicted on a parent/child nested vault structure.

I would recommend pausing Dropbox & Obsidian Sync immediately, then try to navigate the folder using your system file explorer and try to clean the mess up.

If you are successful in cleaning it up, I would recommend setting up a new clean Obsidian Sync remote vault (and eventually deleting the old remote vault) to avoid contaminating the data.

As always, feel free to jump in Discord and we can possibly help debug/resolve this issue in real time.

Hi, so perhaps you can clarify this finally: if I want to use Version History (I bought Sync for that!) and I also want to have my vault in a iCloud folder… how do I do that? You should make clear in the help file Obsidian Sync.

There is a section of Obsidian Sync and third party systems in the help vault