recently cancelled a ticket due to illness

flight was cheap fares (Q and N), ticket was cancelled before first leg, and I have a doctor's note. When I called to cancel it, i was told to go the airport with the note to do the rebooking, since the note would waive the change fees, and I was also giving a "document number" since the CSR explained that my PNR would not stay in the system. the CSR said I would have a "credit" in the AA system for this trip.

so two questions- first am i hosed at rebooking this at all? second, do i have to rebook the same trip, or can i change it? this particular trip was SFO-KIN, KIN-MIA, MIA-SFO all on diff days, and I would rather skip the MIA stop and book it as a round trip SFO-KIN or book SFO-MIA and then MIA-KIN inside that (which seems to be the cheaper thing to do)