So the same thing happened to a friend I applied study permit for. His stamped-passport got missing. So I sent an e-mail to the local visa office that processed his application and they gave the directions as to what he needs to do. He got a new passport and as got it stamped.
But know that, you can't just change your passport, there should be a valid reason else you will be told to submit a new application. My friend had to get a police report to attest to the claim. So be prepare for all that.
