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To upgrade, do the following:

cd /tmp
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.