I think you can, but only if you have reserved a faction slot for that purpose- essentially you'd have, say, two KH factions: the first one, Chremonides' War, and a second one, the Koinon Hellenon, which would only emerge if the Chremonidean faction achieved certain goals.
You can also use the 'Kalmar Union' mechanic to have one faction (presumably the players) absorb another faction through marriage or some other scripted circumstance- but this doesn't change the name.
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