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If you are sure no other files are changed, you could upload your original index.php.
Check and verify your database too.
Is the file manager shown from inside XOOPS?
Then I hope it is strictly reserved for the webmasters group? (Never the less, it is an additional security risk)
Check out your logs (also from protector) and match the dates to the dates of the changed files and try to figure out which modules were attacked and how access to your site was obtained. Try to follow IP's and browser signatures back in time for previous operations.
Ask also your host provider, it could also be, that not XOOPS is hacked, but the server (and vitualization) software, if the hoster is not up to date with his software. He has also a view to more logs and can maybe tell you something about the attack vector.
You are not alone: yexo.bplaced.net, moto-plaisir.fr
All german hosters/servers and the last one is also yours.