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CRITICAL - Directory ID reused ...
This error means, that there exists two resource names in the same directory pointing to the same subdirectory. This can be caused by faulty synchronization (e.g. renaming a folder but the sync client messes up and let the old/former one still exist).
One of the resources (a folder containing a dir.c9r file) can be deleted since they point to the same content, but Crypomator cannot decide which one.
If you are asking, how this is possible: Cryptomator flattens the encrypted directory structure and therefore needs to link parentfolders and their children. If now an encrypted folder is duplicated and renamed to a valid encrypted name, suddenly you have two “resources” in the same directory pointing to the same subdirectory. For more info, read about the security architecture of Cryptomator.