Doesn't sound like a bug.
Companions do take off occasionally as part of quest stages. When this happens, you should get a message saying something like "Cait don't want to be leader of Jamaican Plains any longer." For the settlement, this has the same effect as if you'd asked her to go with you; the settlement will be leaderless and the RotC auto build will freeze. However, the plots already placed there, and the settlers, the recruiting, everything that's part of the base SS mod will continue to evolve as in a non-RotC settlement.
Re finding her, if she's still the active leader, check at the blue print on the city planner's desk, you can always build a bell and summon the whole settlement.