Thanks for the reply falko.
This is what I did to get everything running again.
This can be a lot of work, but with a xml template I could create a webpage that generated this commands for all websites on my system.
First I changed the ssi to 1 on all website in the database with the sql command:
UPDATE `isp_isp_web` SET `web_ssi` = '1';
Than changed the status to u (update):
UPDATE `isp_isp_web` SET `status` = 'u';
Also changed user setting (you can set this back afterwards)
UPDATE `isp_isp_user` SET `spam_rewrite_subject` = '0';
Ans set the status to update.
UPDATE `isp_isp_web` SET `status` = 'u';
Than I ran the command: touch /home/admispconfig/ispconfig/.run
The website user on the folders in /var/www and a lot of subdirectories allready changed. But not all and permissions were still 775 on all files.
To change the rest of the files I did this:
1.
cd /var/www
find . -type d -print0 | xargs -0 chmod 755
find . -type f -print0 | xargs -0 chmod 644
changes all folder permissions to 755 and files permissions to 644
2.
chown root:root cgi-bin
chown root:root error
chown root:root html
chown root:root icons
chown root:root manual
chown root:root localhost
default files/folder to user and group root
3.
chown -R adminusername:web10 --from=apache:web231 web10
changes the wrong user=apache and group=web231 to user=adminusername and group to the name op de website folder (web10 for example). Last is to do this in the folder web10
4.
chown -R :web10 --from=:web231 web10
change all groups that are set to web231 to web10 in folder web10
5.
cd web10
chown root:root .procmailrc
chown root:root .forward
chown root:root .spamassassin
chown root:root .vacation.cache
chown root:root Maildir
chown root:root passwd.dav
changes default files/folders user and group to root
/// Extra. for my CMS I used this to changes the permissions of some files and directories. You can change these to your own needs. This a just as an example (for CMSMS).
cd web
chmod 644 config.php
chmod 777 -R uploads
chmod 777 tmp
cd tmp
chmod 777 cache
chmod 777 templates_c
After changing all the files the server ran fine again

.
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