BTW good luck with ISPConfig... I went to Virtualmin Pro which is alot more friendly to systems then this program was. ISPConfig ate my websites up after a upgrade to the dev version and if its going to do that then its a waste of time for me.
The ISPConfig installer and updater does not contain any code that can change your websites, so you will have to search the problem somewhere else. The installer modifies only files in /root/ispconfig, /home/admispconfig and in the ISPConfig mysql database and I guess you do not host sites in one of these directories.