Hmm, I can only suggest You one thing. For me, I have made an batch connected to qvd, in which I monitor uses of CAL's, and licences to documents. But still, if problem occurs, I have to check my collected data and add everything manually. For You, I think you could backup 2 files:
The links in explorer are correct for my system, you should check where those files are, in your case.
The first one file is located in Your QlikView Server Document Folder, I think in QMC - System - Management Service - QlikViewServers - YourServer - Folder Access or Folders. The second one is main data folder for QlikView, I think in that same place in QMC but just in Management Service probably in Auditing tab. If not, in your case, just search for that files in Your server directories.
Just make an script to backup that files, once/twice a day, when Your users start and end work. If something goes wrong, and your Data will be deleted, You can try compare Your backup files, and the original files during "vanish problem" and then back them up if (when) the data will be missing in those files. I hope I have helped You.