All that will happen is that you will have to recapture depreciation. You will realize a capital gain regardless unless the gain is excluded. No, you don't have to physically move into the space. If it was empty the entire time you owned the house and you never had an office there, it would still be part of your home.
It will be treated the same way as a room in your home. You would be including the expenses for the entire home, on a prorated basis. It is still attached since it is over the garage.
