I know the problem also from my Synologys. It could be that the problem resolves itself with time or if a comparable file is saved again, that it resolves itself.
It may also be possible to fix the problem via the --reset-deltas startup parameter.
Synology is also a special case in some ways. Synology put the DSM over the Linux system and is therefore somewhat unconventional in its handling of permissions. It can therefore happen that such effects occur in this context as well, but this is not always the case. If this is the case or that is not clear, it may help to reset the affected subdirectories recursively root:root with 0777 via console and to inherit the rights in all subfolders again in the DSM in the corresponding root folder.
Since the topics of Synology and encryption have already been discussed in the forum, maybe searching for them would help. However, I would obviously work without encryption if it is running, because the encryption is controlled by the DSM and not by the Linux running underneath.