Okay, rg305,
Thanks for this.
For some reason I see this server listed ad ALIAS on another server, first let me check that.
YES!! that was the problem!
For some reason the apache config was corrupted.
I had another server with alias and certificates "listed" as Linux.vitusdcollege.nl
I got into the apache config and deleted all the "weird" entries.
rerun the automatic certificate renewal et voila.. I got a new certificate!
So for some reason it got messed up, no sure why but you were right: Apache was to blame.
The Dump gave a clue that I could not see in the other web-based configs views.
So for some reason I had 2 virtual server claiming they were the one, and there the problems started.
Thank you again for great support.