Check root folder and Qlikview server folder, look for PGO files, make sure that all of them are in sync, to verify this they must have the same file timestamp ( Date modified). If one iis out of sync, specially the BorrowedCalData.pgo, it will cause you issues. Best to alleviate the issue, is to Stop the Server services > removed the PGOs ( you can delete them or move the off their locations) > start the service again and let the Qlikview Server recreate a fresh set of PGOs; unfortunately, you must add the CALs again.
Default PGO locations:
Root folder / Root application folder: C:\ProgramData\QlikTech\Documents
(Note this location can be manually change, if you don't know where they are you must ask the previous admin)
Qlikview Server folder: C:\ProgramData\QlikTech\QlikViewServer
I have been battling this issue for 10 months. I have research the documentation and could not find any resolution.
I have tested your solution by restarting the server service and all the Named Users as well as the Document CAL Users come back.
The reason for the need to restart the service every week is the Server's memory (32Gb) seems to grow to 20Gb. I have not pinned down the reason -- but back in 2007 I do remember QlikView having issues with memory leaks. The symptoms seem to be the same as memory leaks issues in years past.
At least I am not manually entering (or reentering) all the users after the restart.
I cannot thank you enough.