I realized I forgot to update this situation for those who might be interested.
For reference, here is the original thread: https://community.ricksteves.com/travel-forum/transportation/lesson-learned-the-hard-way-re-booking-a-flight-through-an-aggregator-sorry-long (The topic is closed, so I am unable to update within the original thread.)
Two months after I made the original booking (and, a day later, lost my upgrade with no refund), after numerous unsuccessful attempts to get the airline to see reason, I filed a credit card dispute. The credit card company immediately refunded our money, but on a "temporary" basis while they investigated the claim and waited for a response from the airline.
Of course, by this time, the cost to upgrade had more than doubled, so I submitted a bid for an upgrade that was 60 Euros more than what I had originally paid, but was less than the recommended bid on Plus Grade. I crossed my fingers and waited.
By the time we left for our trip, nothing had happened with my bid. However, the plane travelling from Brussels to Kigali was quite empty, I guess because of the Ebola situation. Rwanda did not have any Ebola cases, but Uganda did (albeit only 20, and almost all of those were connected to people who had been in the DRC). However, the flight does a circle: Brussels, Kigali, Entebbe, Brussels, so anyone who had originally booked for Entebbe had probably cancelled. Also, a lot of travellers combine Rwanda and Uganda, flying into Kigali, because the driving distance to the gorilla trekking areas, including those in Uganda, is shorter than driving from Entebbe. Most of those people had likely also cancelled. So, there were just 7 of us in Premium Economy on our flight to Kigali/Entebbe.
Still, I had no word on my upgrade. Finally, 3 days before the flight in question, I decided to look to see how many seats in Business Class were available, to try to determine the likelihood of my bid being successful. Well, not only were there more empty seats than there had been the last time I'd checked, but BA was now offering upgrades for purchase for 5 Euros less than my bid! So, I cancelled my bid and purchased the upgrade.
The good news is that I ended up with my upgrade for only about $90 Canadian more than what I originally paid, since my Visa dispute was ultimately successful.
The bad news is that it was the worst Business Class experience I've ever had. My main motivation in wanting the upgrade was to sleep, since we had an onward flight from Brussels to Montreal. Because of the stop in Entebbe, the flight service doesn't really get underway until after that stop, which makes sense. However, the stop involved a crew change and a plane cleaning (although we did not have to leave the plane, thankfully), so it was busy and noisy. Then, after leaving Entebbe, dinner was served. Fine. I ate lightly, because I wanted to lie down and sleep afterward, and I did so. Aaahhhhhh! But just over three hours later, the crew started rattling dishes near us, as they were getting breakfast ready to serve. That awakened me. Then, they turned up the lights and served breakfast. Really? Who needs to eat breakfast 3 hours after eating dinner? So, I didn't get nearly as much sleep as I'd hoped, but I did enjoy the box of Belgian chocolates they gave each of us right before we landed.
So, all's well that ends well, I guess.
I still have a claim in with the EU authority for the cost difference between my original upgrade and the one I paid for last minute. I don't have high hopes of getting it, but it's the principle of the thing. I'm not even trying to claim the over $100 Canadian in long distance fees I incurred trying to get things straightened out, and I still lost hours of time dealing with the situation. Sigh.
So, even though things turned out mostly in my favour, I will never book through an aggregator again, and I am closing my Booking.com account.