When upgrade package database setting ( from file config/db.inc.php) misses protected, in result update brocen. Please mark config/db.inc.php as config file in ebuild, and include in CONFIG_PROTECT
1) You can set USE=vhosts to make sure the live web root isn't automatically updated. 2) You can set CONFIG_PROTECT yourself on any file or directory you like, as seems fit to your system. 3) webapp-config helps you update those protected files properly. *** This bug has been marked as a duplicate of bug 243260 ***