There shouldn't be a plug that he missed if the rest of the radio works as usual. The CD player doesn't have any separate harnesses.
It's possible that unplugging it/plugging it back in killed something in the CD player; that happens sometimes with electronics (though it's unusual) if the battery wasn't disconnected first.
I would actually guess that it's just a coincidence that you noticed it not working a few weeks after the heater core replacement. They probably aren't related IMO.
MODS: PW TMIC, Cobb catted DP, HKS cat-back, AVO filter, Bren e-tune; Konis/Epics, Advan RCII