So last week I tried to upgrade an upcoming flight to EMS on a blue fare which was booked using the covid healthcare heros certificates. Seat selection did it's thing and after processing, the itinerary now shows us in the new seats. however there was a banner error on top of the page that said error processing payment for more info call the 800 number. well hold times were over 1.5 hours so i'm not inclined to do that.
I saw the pending change on my amex but it has since dropped off however no real charge is posted. looking at the itinerary it shows us in the new seats and at the bottom of the page I see it says charged to american express ending in xxxx with the amount of the upgrade.

Since i got a confirmation email is it safe to assume i'm good? Any chance I show up at the airport and they stick us in 2 middle seats?

If you want to confirm without waiting on hold, I'd suggest either Twitter or iMessage (use the "Start a Conversation" link here).

I upgraded 2 flights last week and got the same message but travelled over the weekend with no issues. It might just be a false error message.

You won't lose your seat assignment until the reservation goes to gate control at the very minimum. They can take payment for the EMS seats at the check-in counter.