I hope he pulls through whatever may be wrong.
I had a betta who eventually only started to flare from one side. He was fine though, and I never figured out what may have happened to cause the other side to stop. Must've injured it on something obviously.
Maybe this is what happened to your betta.
There anything he could've scratched himself on, fake plants, decor, etc etc?
I think you're definitely doing the right thing right now though w/ the meds.