Guaranteed prize chips are deducted from your account because that is why that MTT is guaranteeing. Participants will win those chips at the end of the tournament and will not be refunded to the manager.
For example:
If your MTT guarantees 100 chips. Buy-in is 1 chip. You need 110 participants buying in, rebuying, and adding-on to reach your 100 guaranteed prize pool.
If the guaranteed prize pool (with rake) is reached then those original guaranteed prize chips will go back into teh club's bank.