I know this can happen in installations that have a very large number of CALs and users. I don't know why this happens, except that the software may be shaky. Are you using a not-too-recent SR with hundreds of users.
The basis for disappearing assignments is usually a corrupt CalData.pgo QlikView Server configuration file.
Make a backup at regular intervals, and copy the backup file back to the document root and restart the QVS.
If this happens more than once, you can consider switching to dynamically assigned CALs and user permissions in Section Access. That way, users with permission to access documents will be managed by Section Access and not by the QMC, while whenever the CAL assignments disappear, they will be automatically reassigned when a user revisits a document. Not worth the effort if you have <100 users, I guess.