Yes I don't have the files from /etc anymore.
I was able to recreate everything by setting up the web with the same settings as it was except the users, after that I restored /var/www.
Now the website worked, but none of the mail or sql dependant pages.
So I restored the mysql databases, including the db_ispconfig and mysql database and ISPConfig actually did recreate all users in /etc/passwd but not in /etc/shadow.
So this is lost and I will have to ask all users so I can set up their passwords again manually.
For the future, what is a good backup plan for ISPconfig? to be able to recover quickly?
I'm thinking in the terms of rsync to a second drive or file server.