While we're waiting on an RPM update that doesn't replace the config file with the default, workarounds are:
1. If you haven't yet updated, save a copy of /var/www/atmail/libs/Atmail/Config.php and restore it after you've updated to 1.05 (Note that I haven't tested this -- it's possible there are some new config variables that are required which are not available in your old Config.php file)
2. If you've already updated and lost your original Config.php file (like I did), make the edits described on this post
to fix your new Config.php file.