> Federated rooms continue to exist if a server drops off

That doesn't answer the question.

How are you resolving things like... user name collisions when the servers reconnect?

I am not the owner of the project, I just use it. Federated rooms have no owners, there will be no collisions (they would simply merge). Nicks are tied to their own servers, and hence unique and will not collide.

This has been an issue for as long as IRC itself has existed. There are solutions to resolve such "netsplits" and "netjoins", but they all rely on the servers in the network being trusted and not malicious.

With Parley, where anyone can bring their own instance, and they are not guaranteed to not to be malicious, that could be an interesting issue to solve.