Are you curious what might happen if a hacker was in control of your computer? The question really is “What can’t they do?”
Until the migration from IM to Skype is complete, I think it’s likely to see both accounts for many friends. It’s simply that Skype, the program, is logging into the both Skype and Microsoft Messenger at the same time.
The most important thing is to determine which messaging program the people you want to talk to will use.