I think they can coexist.
However, if you removed the directory from icloud in one computer, it’s possible that at tha moment Icloud deleted your files.

I think that I’m having the same issue with Sync on Obsidian v0.10.13 (AppImage). I’m running a Debian-based OS and my Obsidian release is fresh (MD5: 3c7f470ac97abc83c172d6844920ab03). I do not have any other plugins installed. Every time I close Obsidian, 1-3 files are being deleted at random. None of the files effected have been modified recently. For the sake of troubleshooting, I pushed my notebook to a new remote vault: The issue is persistent, and many of the files being lost have no version history and have never been deleted prior. Before exiting the application, the status icon has always shown that the files are fully synced. There are no exceptions raised in the error log. There are no other programs installed that should be interfering with my files locally. The missing files are not being moved into my system’s recycle bin or the vault’s .trash directory. The version history has saved me thus far, but every time I open Obsidian I have to go into Settings > Sync > Deleted Files and recover a few files tagged as [deleted] a few seconds ago. This behavior only occurs when Sync is enabled. I haven’t experienced any problems while the plugin is paused or when working with untracked vaults.

Thanks for your report. Did you notice any pattern in the files that are deleted?
Do you use obsidian sync only on one computer?

@Jevin if you care reproduce this problem reliably, you could really help us nail it and solve it.

Thank you for the detailed description. If I understand correctly, that means somehow Sync is deleting the files on application boot-up (rather than shutdown?) based on the timestamps. If you read the vault folder, right after closing the app, do you see the files disappear, or does it only disappear once the app boots up?

When you boot the app up, and view the sync log, do you see it say “Deleting remote file …” for the files that have been removed?

(Also just following up what WhiteNoise said, any patterns in the file names perhaps, special characters, or maybe just a long directory/file path?)

Sorry for the delay guys. I’ve been very busy and it slipped my mind. I was only taking Obsidian for a test drive, so I did not retain those vaults for any further testing. I do still have screenshots of an example (albeit not a particularly useful one) from the other day though. I’m preoccupied with PWK/OSCP right now, but once I finish I would be happy to help troubleshoot.

And yes the deletions were on application startup. There weren’t any special characters or anything in the absolute or relative filepaths. I think I opened my first vault in Windows once, but that wouldn’t explain the second vault.

obsidian_ticket_ref2-hist

Oh yeah just to rule out possibilities, were you using any community plugins?

And also, you said the files were deleted at random, but was there any pattern as to which files they might have been? Possibly related to having them open/navigated to, etc?

I doubt this is of much use but wanted to document. I’m running multiple vaults in Sync with a MacOS Big Sur installation and a current Windows machine. Stumbled onto 2 files this weekend that had disappeared from my vault. I did not delete them (not knowingly!) as they were both large Index/MOC type notes. Both represented a lot of work and I was pretty stunned to hover over an internal link and see “file not yet created”.

This was not the disaster it could have been - the windows machine has not had Obsidian opened since last Wednesday. I was able to remote into that machine and copy the .md files for each from the folder they reside in over there. Tomorrow I will back up both vault folders before opening Obsidian on that desktop just in case more files are missing that I haven’t discovered yet.

I realize this is not much help as a bug report as I don’t know when it happened or have any ability to reproduce. Just wanted to document for reference. This occurred sometime after Wednesday noon Jan. 27 and prior to Saturday noon Jan. 30. I’m always using the latest insider release so I was on 0.10.10 for the early part of that time period then updated to 0.10.11. I use several community plugins.

Is this vault being synced by other backup services, like iclould, dropbox, google drive?

No other backup services.

I don’t know how the history feature works? I have already recovered the files and copied the new versions into the vault.

settings->sync
delete files
and also view
sync activity?

Do you syncronize multiple different physical vaults to the same remote vault?

Can you clarify what your setup is?

When I go to sync -> view deleted files I do not see those files in the list.

I have Obsidian on my home MacBook Pro running Big Sur. There are two vaults on that device that are each a synced vault. I have Obsidian on a Windows Desktop at work that has two vaults linked to the same two sync vaults.

How many remote vaults did you configure, one or two?

There are two remote vaults. I have not had one of those open in this time frame. Both lost files were from a single vault.

Also - I have been doing a huge amount of work the last few days. The sync log does not go back past this morning when I pull it up. As I said previously the view deleted option does not show the files being deleted in the time frame I know they had to be.

Is your vault on you mac synced now?

It says it is, sync log shows activity including my last edits.

if you take one file out of your vault and let it sync, does it appear in the deleted files list?

Take it out using file explorer or delete in Obsidian?