This is not a definitive answer, and maybe somebody else has more experience with this particular issue. However, I will tell you what I think based on my experience with COPA:

First, I would not sweat it immediately, and I would give the system a couple of days to sort it out. Not everything happens instantaneously in the COPA system. They seem to fix things with a batch process every so often. If they have you on the upgrade list, then it is very likely that you will have a seat in clase ejecutiva when you fly.

Lately, COPA seems to be making only "C" (full fare business) available in their system until just a few days before flight time (I look at a lot of IAD-PTY for my routes). They seem to only open up "D" (discount) and "I" (upgrade) 48 hours or less before flight time. I think your worst case situation is that the itinerary won't change in the COPA system until a day or two before the flight.

If you want to push the issue, I would call UA and ask for the Star Alliance desk. This will send you to a Customer Service Rep who specializes in working with other *A airlines. It is my understanding that they often resolve issues that regular CSR's do not know how to solve.