Actually, I think that may be a result of them using mounts. Any ship design that uses a mount will not be saved with the empire file, even in stock SEIV.
Mounts and mods. I keep running into the problem so I know.
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Creator of the Star Trek Mod - AST Mod - 78 Ship Sets - Conquest Mod - Atrocities Star Wars Mod - Galaxy Reborn Mod - and Subterfuge Mod.