You should call again and ask for credit for the COS-DEN flight and explain that the agent at the bus took the BPs, etc. It may take several calls.

I don't know that there is an official policy, per se, but I have rarely had problems getting "original routing credit" due to irrops; I once did have to call 3x times (first two agents claimed "the policy changed"). If you can get a non-ICC agent, that would help, too (tougher as a 2P, I know).

Sometimes, it has paid to keep my rerouted credit (as the often-full-Y flights have yielded more EQM than the original itin), but if I read your post correctly, you were in full Y to begin with, right? (And thus should be due 750 EQM for the COS-DEN flight.)