Can servers A and B federate, and then separately C and D federate?
Yes.
If so, can A B and C be federated, but separately C and D be federated, so D is not recognized as federated for A?
Yes.
If A, B, C, and D are federated, and it becomes apparent that D is a bad actor, how does D become defederated?
A, B, and C each individually decide whether they want to deferate with D. Maybe they all do, or maybe only some of them do. It's analogous to groups of people deciding who they want to be friends with.
At least that's my understanding.