Database damaged repeatedly after deleting files in indexed folders

I’ve been having to “Verify & Repair” my database a few times a week. I have an indexed folder of plain text documents and markdown files. I use an external editor and sometimes create an “Untitled.txt” or “” unnecessarily and delete within a few minutes of creation. The next time I attempt a backup (Export → Database Archive), I’ll be told the database is damaged. I’ll find the file within Devonthink and move it to the trash, then clear the trash, then verify & repair, and all will be well.

I would expect Devonthink to sync with the filesystem and understand a file had been deleted. Is this expected?

DT is not able to capture all file system events (I think it is a macOS notification issue). But there is a very easy solution for that: select the indexed base folder and go to File → Update Indexed Items or press Option-Command-S keyboard shortcut. It updates the indexed folder and you don’t need to verify and repair.

Which version of macOS and of DEVONthink do you use? And what’s the path of the indexed folder?

I’ve had this problem as well! I’m on the latest DT update and use Big Sur.

Welcome @drmeeshelle

What is the path of the indexed folder in the Finder?

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It’s happened with many of my indexed folders with different paths, but for example:


At first I thought it was because it was dropbox specifically but I’ve found it with other folders on my drive that are not part of my Dropbox as well.

Are you using macOS’ disk management feature to put the desktop and documents folders in iCloud drive?

The automatic update of indexed items located in cloud folders like Dropbox is limited, deletions can’t be automatically applied to the database.

E.g. this could be the result of someone using Data > Move into database on another Mac synchronized back to this Mac by the And this shouldn’t be applied to the database as it would cause data loss.

Therefore you just might have to use File > Update Indexed Items on your own.

I’m on Catalina, Devonthink 3.6.1, and the path is something like ~/Dropbox/Notes/, but also occurs with ~/docs/clients/bar.txt (not in dropbox nor any other syncing program).

For dropbox, I’m the only user, no files are shared, and for the time being, I never edit anywhere other than my main computer, so nothing is syncing from elsewhere.

I too am the only user that works with this, and while I do in theory use another device to access the data generally speaking I’m only on my desktop and this issue occurs when I know I’m the only person handling the data. That being said, manually refreshing is a solution that works well; I’ll be sure to do that more frequently.

@BLUEFROG, I don’t use the iCloud features, so it looks like it does happen with files that are just local too, as seems to be the case for @kmg.

So you are syncing this database?
To DEVONthink on another Mac or DEVONthink To Go?