Confirm again that the new passport has same number as the old???? This shouldn't be the case!!!!
I would say don't send in a copy of the new for now. Once CIC sends your PPR, send the 2 passports (old + new one). Certainly CIC would never issue a visa on an expired passport so the agent handling your case would know the meaning of receiving a renewed passport with the old one initially used in your application.
Come to think of it you have never read where CIC said notify us if you renew your passport. But they do say notify us if you have change of address or new birth or married.