I discussed this with the other developers and one remembered a similar case: Files not available except when using Android App
We fixed a bug in our synchronisation conflict resolver for 1.4.10. So if you updated to 1.4.10, the faulty resolve stated the same.
! Before you execute the below command, read the whole post and make a backup of your vault !
The shell-commands given in the other thread are only for linux and mac, so i figured one out for powershell/windows:
Get-Childitem -File -Depth 3 -Recurse | Where-Object{ $_.Length -eq 36 -and $_.Name -notlike "0*"} | Rename-Item -NewName {"0"+$_.Name}
It finds all directory files, which are not marked as such (size of 36bytes but no leading “0” in the name) and adds the missing zero.
You need to start powershell and navigate to the d folder of your cryptomator vault. Then enter the command and hit enter.