I can’t tell you, which version of Cryptomator I used before the current version, but I’m pretty sure that this problem didn’t exist with the older version. My current version is 1.5.11 (exe-190).
When I try to delete an empty folder everything is fine, but when I try to delete a folder that is not empty, then all the files inside this folder and all of it’s subfolders are deleted, but all the subfolders and therefore the parent folder are not deleted (because it is not empty).
I can navigate inside of the not deleted folders until I reach a subfolder which only contained files (and no subfolders). If I try to enter this folder I get a message telling me that this resource is not reachable (translated from the german language message).
When I lock the vault and enter it another time (next day), then I can enter the same folder that brought the message the day before. And I can delete all the folders that were not deleted the day before. But only as long as they’re not containing any subfolders.
So have to get rid of all the subfolders one by one from bottom to top, until I’m finally able to delete the parent folder.
I found one topic from 2018 describing the same problem, but with Linux. And the problem wasn’t reproducible there.
Oh, and if it matters. I tried to delete the folders with the default windows explorer and with Total Commander, and I had the same problems.