Entirely removing flight above a certain altitude would be difficult. At minimum it would certainly devastate the bird population. Gliders for low energy environments. Rockets for vacuum environments.
Within that 200 years, something went wrong causing the planet to lose atmosphere. A planetary shield was built. It doesn't follow the terrain contours, intersecting with mountains and such. It's ovoid in shape, keeping with the average ovoid shape of the planet. It only keeps gasses in; liquids and solids can get through it. Now that 200 years has passed, the shield still works but there's no atmosphere above it.
Artificially Intelligent, Self Replicating Anti-Aircraft Guns
The thing about AI is they are single minded and goal driven. The goal they are built on is the one they optimize for. The planet, at one time, needed a really good AA defense. One was designed and built. It includes factories and mining capability oriented towards the ability to replicate and upgrade. It's only interested in keeping the skies free. It's constantly building new, better AA emplacements. Birds were considered necessary at the time and it was easier to "teach" the AI to shoot down fast flying things rather than teaching it to differentiate between a bird and a slow drone. Localized defenses around the emplacements prevent sabotage.
Decades later, they have AA beyond anything the current population can design. It's entirely AI driven and, after a long period of getting stuff shot down, nobody bothers with high speed aircraft any more. (Though there is a kind of race to see if one can build an aircraft that is faster than everybody else but won't be targeted by the AA. It's very entertaining. Occasionally somebody produces something with a combination of dexterity, speed, and stealth needed to avoid the guns and win a race, but it doesn't last very long before the guns advance enough to take them out, usually a few days. The bets on how long they'll last can get pretty high.)
There's no flesh and blood people ever since it was discovered how to upload your brain. It's been like that for 200 years. I was one of the first generation. I remember what it was like but it's better in here where you don't have to hurt or grow old or see family die. We still have our wars but they're done in the Games now. Everybody wants computing power and memory space so those are the rewards but everybody works towards creating more computronium. Though, it's mostly automated now.
I do miss somethings. Space doesn't really exist anymore. Sure, you can go out there, but there's nothing to go to. The stars, the planets, our sun, they're all just paintings on a background you can never reach.
Flight is limited but it's not such a big deal since you can just teleport everywhere. There's no supersonic aircraft since they eat up terrain generation CPU time like crazy. Biplanes are fun but they don't get very high. (The Realists say it makes things more realistic, but the rest of us know it's because the governments use the clear areas for top secret research and such.)
Most people today don't know it, but they never quite got the taste of chicken right.