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Virus gone bad

Last Modified: 2013-11-22
ok so last week my boss got a new virus,, it took out all his desktop items and all his my computers and admin programs. I took is hdd and slaved it to my pc and performed a scan with 3 different virus scanners and they all came back ok so i proceeded to manually look for the virus and unfortunately i found it so it took over my pc and i ended up loosing alot as well. I did get the file to essentials who found that no one had been recognizing the virus as a virus so they immediately pushed out a update and i was able to scan find and delete the virus. but that is no my problem, my problem is that one my boss pc all menu items, admin programs(everything in the admin tools folder) are gone, as well EVERY file was hidden.  what i need is to get it all back, there are files listed in the start menu but when you open it up for example smart defrag> empty is what  i get. on my pc it also removed some items but not to the same extent. what can i do i would hate to have to reload two pcs,(i did try a restore to a differnt restore about 2 weeks back) and that had no effect.
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