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As far as your instant messenging programs are concerned, once you get rid of the trojan, virus, or spyware that's infecting your system all you should have to do is reinstall these programs either from a backup or just redownload them and then log back into them with your original username and password when you connect to the internet and you should still have all your contacts because I believe the contacts are stored on the webservers of those programs and not just your harddrive.
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