I had ISPConfig working, set up some sites, tried to update, now ISPConfig is no more. I only used it as a mail server and the mail still works despite the fact that ISPConfig does not. Do I need to erase any directories (ie. /home/www/web*) if I do a fresh install of ISPConfig or does it automatically replace them?
No, you don't have to erase anything. ISPConfig install should do everything automaticaly. Is ISPConfig running? try /etc/init.d/ispconfig_server restart and if it doesn't work reinstall ISPConfig and check if there are any errors.