This seems (almost) completely unrelated to BoxCryptor.
Such a "versioning" feature would need to be part of the synchronization-tool being used(like DropBox).
Only if encrypted file/folder names are used in BoxCryptor,
the potential addition of a suffix by a sync-tool would need to be
recognized and supported by BoxCryptor.
This problem applies equally well to real versioning tools or backup tools with some form of versioning, when used in combination with encryption.
The main challenge there is that there are so many methods of (semi)versioning around.
If BoxCryptor would want to support these all ...