Removing duplicate notes created by Sync

I have vaults on my PC, Mac and iPhone synced using the paid Obsidian Sync feature.

Inside the Vault are some folders with notes in and some notes outside of the folders. No folders are excluded from the Sync.

Yesterday something weird happened and the iOS app has made duplicates of all the notes in my folders in the root directory.

The root directory now has all my files which were not in folders mixed in with (unwanted) duplicates of the files from the folders.

My first priority is to undo the damage and remove those duplicates.

Is there some way to do that which doesn’t involve manually going through a list of 10,000+ files one by one and checking whether it’s a duplicate that needs deleting?

Has the name changed to something unique? You could filter and move them with the Windows explorer. (top right)


No, exactly the same name unfortunately

If the duplicates’ “last modified” dates match when they were created (instead of the dates of the original files), then sorting by date would help.

You’re not using Sync with another sync solution (like iCloud), are you?

I suspect that’s what caused the problem. Honestly, I probably had iCloud Sync and the Sync plugin running at the same time on one of my machines without realising

Thanks. That’s a good suggestion. I had a quick look and some files have a last modified date which matches the date of the error. But it’s confusingly inconsistent across different devices and there’s the occasional one that doesn’t seem to make sense at all. I’ll spend some time looking through it in detail and see if I can make sense of it. Hopefully I can use this method to deal with the bulk of it and then do the last handful manual. Thanks again!

I think if iCloud is only on 1 machine it’s OK, but if it’s on more than one then it’s syncing and Sync’s can clash.

That doesn’t sound like a good idea at all. Avoid mixing sync tools, period.

I’m not promoting, it, but I’ve seen it said more than once that if you use iCloud on one and only one computer — so it only syncs with Apple’s servers and not with any of your other devices — it should be OK (and any other mixing is asking for trouble). I’m pretty sure the people saying it were at least regulars, possibly mods or maybe even one of the devs. Frustratingly, I can’t find any of those posts now except this one from WhiteNoise Using Version History: using iCloud and Obsidian Sync simultaneously? - #4 by WhiteNoise which is the other way round — using Sync on one only 1 computer for its version history.

I only mentioned it because the poster’s phrasing sounded like they might have had iCloud active on only 1 computer. I wouldn’t normally bring it up when discussing sync options.

Probably some warning in the app would be useful and fairly easy to implement here. If the vault location contains ‘iCloud’ and you try to turn on Sync it warns you not to?

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