I would try changing the litter if you think it could be that. My boyfriend and i buy cardboard based litter for our bunnies’ litter boxes. If you dont want to go out and buy cardboard based litter, you can buy cardboard boxes and shred them up to use too. Layer the top of the litter with hay so the buns arnt tempted to try and eat the cardboard if your buns are big chewers
Other than that, how dry is it the room your rabbits are in? Ive noticed one of my rabbits skin flakes on days its very dry in our apartment. We kick on the shower on high heat for about a half hour to make it more humid, and that usually stops the flaking. We used to have a humidifier, but it got clogged and we couldnt afford a new one, which is why we use the shower instead. I suggest this because dryness can also cause a rabbit to wheeze a bit if they arnt used to air that is more dry. It could also be the temperature if your place is a bit on the warmer side, that cou,d cause breathing stress and cause extra shedding causing your other bun to be itchy more often