Thanks for you help, now it seems that this isn't the main problem anymore. The CP just broke the sites. The siteManage is broken too:
This returns a 404 error for all Virtual Hosts:
http//w w w .server.com:81/.cobalt/siteManage/ w w w .server.com/
When I make new Virtual Hosts it works, though I just noticed a new one is now broken too.
Just a guess, but I think some files the CP needs are corrupted, is this possible? Any way to fix this? Getting stressed, because many sites are hosted on this machine.