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Skype doesn't actually sync with Address Book. If you permit it, Skype simply accesses Address Book. If you wish to maintain the two in isolation from one another, you'll need to enter the ones you want in Skype directly into Skype.
An aside: if you wish to maintain the privacy of your Address Book (yea, verily, even all your files) to prevent students from accessing it, be certain to select a robust password for your computer--one that's not easily guessed. Students seem to have an uncanny ability to get where they want to go with technology.
Yup; I'm a recovering educator...