I was having a similar issue with my Sony Bravia Television remote no longer controlling my Apple TV all of a sudden but I have found a temporary solution that’s worked for myself. The Sony remote can work via both Bluetooth or IR. To fix I followed these steps on the Tv itself. Settings - Remotes and Accessories- Bluetooth Settings - Toggle Bluetooth to Off. This will force the Sony TV remote to Use IR and allows it to be picked up by the Apple TV. You may have to relearn the remote in the Apple TVs settings but It worked straight away for me.
Only slight issue is that now when you try to control the TV itself e.g. change brightness settings it is also controlling the screen of the Apple TV as inputs at the same time. However not an issue most of the time.
Hopefully Apple Fix the issue so that I can use my Sony remote to control the TV the way it used to but this solution will suffice for now.
Hopefully this is helpful.