A problem I have seen is CAL's disappering on the reboot of a server.
The normal solution is to delete all pgo files in the Root Folder (User Docs Folders)
AND the copies that exist in Program Data\QlikTech\QlikView Server.
Before you do this you must stop all 5 (or 6 depending on version).
It is important you delete both sets as they recreate from each other.
Also important you stop the services so that they are not in use and are deleted properly.
Restarting the services will recreate the files and you then reallocate the CAL's to the document. They should now stay following a reboot.
I have 1 client where this appears not to have worked but I have more where it has fixed the issue.
Good luck Philip