The most important part of the federation process is played by whichever instance hosts the original post. They’re the hub and all other instances are the spokes.
So once Instance A defederates from Instance C, nothing Instance C users add to posts hosted by Instance A will be added to the master manifest. Basically, everyone is updating Instance A’s copy of the post, and that copy is then being redistributed to all other federated Instances.
Once Instance A defederates from Instance C, the only time their users will interact from that point forward is on a mutually federated instance. Both communities can comment and interact on a post hosted by Instance B.