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I would say first, make sure your system has the best security out there. After that, try reinstalling the System module. That might bring your modules back up. If that does not work; backup your mainfile.php, clear out the directories, and then reupload everything including your backed up mainfile.php. Do not go through the install process or you will destroy your MySql database. Then reinstall your modules, any hacks you made, and finally install GI Joe's Protector. It is important though to make sure your server is secure or they will just hack it again.