R is used to indicate 500-mile and complementary upgrades and C is used to indicate SWU or Miles upgrades. Your original fare class survives in the system and in my experience it only gets lost when you have to be switched to another flight if weather or mechanicals get in the way.

When the upgrade happens 4 days out (or maybe even 2-3 days out) you travel agent still owns the ticket and so an upgrade notice goes to them and they have to do something to confirm it I believe.

Once I looked at my itinerary in my corporate TA website before they had confirmed acceptance and I had three entries on the same flight - one in Y, one in R and one in C! The C and the Y were marked as cancelled and a few hours later only the R remained.