If the file was open during the install of the new version, that at least is a special situation. In that case the upgrade in a way could be related, although it’s a very special case. We have not tried stress testing that particular scenario, but what does happen is that the new software will initiate an uninstall of the old, and that uninstall will in turn ask any running processes to end. It’s supposed to do this in a nice and orderly fashion of course, but it’s not impossible that something could go wrong here causing the old AxCrypt to ended prematurely while writing the updated encrypted file.
I do not recognize this situation at all, it’s actually a first that I’ve heard of, so it’s certainly a pretty isolated case. Still, I’m very sorry for the inconvenience. We do try to make the software as reliable as possible in as many situations as possible.