To upgrade, do the following:
cd /tmp wget http://www.ispconfig.org/downloads/ISPConfig-3-stable.tar.gz tar xvfz ISPConfig-3-stable.tar.gz cd ispconfig3_install/install php -q update.php
You still have to change .htaccess files or other apache config options you may have added manually.
You can have ISPConfig rebuild the vhosts files by going to Tools -> Resync.
Upgrading from Apache 2.2. to 2.4.7
Fixing a broken ISP Config installation
Do the upgrade process and answer YES to let it reconfigure services.