I did a DB Backup and a copy of the alf_data directory. The main problem behind was, that wcmqs is not updating properties of some files (not all). I can change names, titles, etc of the nodes, but wcmqs does not update the view. So I set up a test system, where I copied the original files into (Cold Backup procedure). It took some time, but the test system is now exactly in the same shape than the original server. I did some tests and a full lucene index at start time. The curious thing is, I can see the lost category with all its children in the node browser, configured in the same way than the other custom categories. This leads me to the conclusion that my problem is related to some sort of caching of cmis:
WCMQS does not update the file properties - wcmqs is full cmis related
The category browser does not "see" the lost category, because I think it uses cmis also
All other custom added categories are found in Share, WCMQS and via CMIS. I really have not idea which way to go.