from what I remember reading about the differences in the mesh (ship shape) there is an additional line in them, as for the entity files the best answer would be to use either a tool like beyond compare or notepad++ to compare the frigate & capitalship entity files between diplomacy and rebellion and add the differences to the entities that you want to transfer.
and there is also the get an answer thread here in the modding area, if you post your specific questions the various modders will probably help you solve the problems
hope this helps
harpo