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Did you installed the app using flatpak?

Then this post should help:

Cryptomator flatpak doesn't find safes

Hello @nullproblemo I found your post in a search because I am having exactly the same problem on Manjaro. Previously used the AppImage, everything was fine but the Flatpak wouldn’t find my vaults. It is, I think, a problem with the Flatpak build permissions. The build doesn’t have access to your mount point, but there is a way to add it - but I came on here because I found that the change would automatically get reversed and I’d have to run the command again. You can give the Cryptomator Fla…