I would take him into the vet to have it checked out. It could be mites or an infection. Some ear mite remedies are available over the counter- but they are strong and usually harsh to kill the mites and when these are applied to an infected ear- it can really cause more pain in the ear- especially as most seem to have alcohol of some type in them too. So ear mite remedies can make an infected ear more painful and won’t help the infection at all. And most ear infection meds are prescription- but even if you happened to have them- 99% of ear infection meds don’t help ear mites at all.
Ear mites can be spread between pets- especially cats and bunnies- so you should get him in as soon as possible to make sure it is not mites. If it is- it sounds like maybe the new bunny might need to be treated to? or at least looked at? But start with the one scratching and your vet should let you know how probable it is the other rabbit could have the same problem.
I work at a vet clinic- and we had a client that had a cat that had scratched it ears practically bloody from an ear infection. They decided to try a pet store remendy of ear mite solution before bringing the cat in- the poor kittys ears were fire engine red from the infection and the harsh meds applied to open sores. We had to sedate the poor kitty just to be able to clean all the mite medicine and infection debris out of her ears.