Remember that having multiple accounts, each with a separate registered email, and each with a city on the same world/server, is not against the rules, so long as these cities do not interact together in a way that benefits one city over the others. Pushing KP is one way to violate this and having multiple cities in the same fellowship could also violate this, depending on how they interact. So if one player has two cities in the same fellowship and plays them equally and keeps any trades or KP exchanges between them equal, that is still okay by the rules. But if that same person removes one of those cities and brings in a FA-only city, then that person is now making the city still in the fellowship an obvious favorite and is now violating the rules.
And that is what the OP makes it sounds like for that fellowship, because why would someone remove their only city in a fellowship, just to bring in a FA-only city? There would be no benefit from that for their main city, so I seriously doubt those three cities swapped out for three FA-only cities was done in a legit way. Also, long, flowery "explanations" by a member of that fellowship only makes it seem more suspicious, not less, since from past experience, that is the exact thing a cheater would do/say. Now, in the end, does cheating really matter? No, unless maybe if the cheating helped a team barely win the FA, or if someone found a way to cheat and finish 1st in the tournaments. Nothing is at stake here beyond pride and the obsessive need to come in first, both of which are sad reasons to cheat.