I assume that they could refederate under a new domain name, but I have no idea how the Threadiverse deals with an instance changing its domain name. Probably not well.
That's going to be a nightmare honestly if they do. Since there are so many Servers now with a big stick in their ass about defederation and only Defederated Hexbear after a lot of persuasion. This will probably end up giving their instance a second chance on many instances which defederated them before.
I was less thinking "they might become refederated and have content reach instances that wanted to defederate" and more "what happens at a protocol and database level if one just changes a domain name, updates the X.509 certificate, and then refederates?" I mean, I don't know how other instances deal with that, whether it can create problems. IIRC from past discussion, there are user keys somewhere in the protocol, and I assume that those would now be identical and collide across old and new instances, for one...