Don't you worry, I was totally aware that the hold operation we were going through the last 500 posts was quite a bit risky without having a restore point to rely on. Yet I apologize the ending of this thread leading to install the system from scratch...
However the new Server was set up in less than an hour, the files were on a seperate drive so nothing to worry about. We managed to get the system running again so we can go back to business as usual.
Well, and now there are over 170 pending updates waiting to be installed, so no time to loose ;-)
What I'm still courious about is what could have caused these system file corruptions (and the last error that leaded to the BSOD), could this have been caused by one or more unsuccessful installed updates, do you have any assumptions?
During the install process I noticed that on the system drive there was enough unallocated space (265 GB) so we installed the system there, which means the old system still exists and for now shows up as drive (F:). The VM also is still accessible - so could we get the "old" system running again?