It had the frigate selected as if you were starting over? You mean the fletcher class?
It sounds like your BO has had a ship tree reset, but I can't be sure from your description. You can just select whatever ships you want. So Fletcher, Somers/Gearing, DDX, Atlanta, O type, S type, Barracuda.
If the BO has ships up to the barracuda SS selected then he should be able to use any of those ships. If he already has his ship tree set, selling your Barracuda and buying a new one, or putting it and/or your BO in the HQ and removing it.