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First, I would re-evaluate my back up procedures.
Second, I would re-evaluate my server hardening.
I've had some script kiddies use holes in programs like PHPNuke and phpBB2 to get a shell script on my server. From there they started putting stuff in places to get back in should I find it. I was worried at first, but turns out my provider had taken some pretty amazing steps to protect my server.
One was to jail my /tmp directory and move it outside the primary server. I'm on a VPS, so this is possible. Guess what, they had scripts set to run DoS attacks on other sites, but they didn't work. :-)
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