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Move the entire Freelancer directory or path to the exceptions list in your anti virus software. This should keep your AV software from thinking that Crossfire has viruses or is a virus itself. It's a rather common issue, and it's being worked on.
It's an animation of a clay blob chewing some bubblegum.
There is most likely an option somewhere in the software that allows it to automatically delete any files that it deems a threat to the safety of the computer, and that's probably why it deleted everything. This is actually a common option in many different AV programs, as it saves the user from having to delete an infected file themselves whenever they find one (unless it can't be deleted, but that's another issue entirely).
Just reinstall everything in this order:
Freelancer Mod Manager -> Crossfire 1.8 (Only install to the FLMM directory, DO NOT ACTIVATE YET) -> Freelancer
Once this is done, add the entire FL directory to your exceptions list in Avast, and then activate the mod.
Avast AV usually appears to be very Crossfire friendly
at least the professional version did not cause any problems to me
A lot of us CF players are battling our AV programs on a daily basis. After following all the necessary steps for installing the mod and adding to my exceptions list, my AV program(F-Secure) continues to once in a while quarantine my CF Exe. It even started to quarantine my restore points that contain my CF exe files. 
Your situation sounds like a real virus, so you may want to do a complete scan and removal before you do any installation of CF like Bugma suggested above. Run your scanner and removal a few times to make sure it removes it, and check your startup configuration to make sure it isn't reoccurring.
Also, you may want to turn off your AV program before you install anything first.
Good luck
Also, you may want to turn off your AV program before you install anything first.
Good luck
More importantly, and as a general rule, scan whatever you plan on installing before you actually install it.
Good luck.
You need store your Freelancer ID and if you played SP your saves. Next try if your PC works windows update ... if yes, download latest update, if no, it look you have real big troubles and this is nothing to do with CF. Next try scan your PC with AV, you can try also use HijackThis and post log at many forums with AV problems ...try little search.If you solved this all successfully, my advice read FAQ about installing CF and follow instructions.
