Recently experienced an issue on Romulan captains aligned with the KDF.(Did not affect standard Fed, KDF or Rom/Fed toons)
The active starship loadout would be copied onto/over the active small craft, effectively erasing its original loadout and any equipment slotted on it.
Dry docking the starship, then switching to the small craft in space and then selecting another ship on the ship manager allowed me to also dry dock the bugged shuttle- which restored both ships.
However loadout items from the small craft were erased in the process.
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Also, my star cruiser was suddenly an advanced escort (Prometheus class) but when I loaded it, it was still the star cruiser. But with the loadout from my advanced escort including the experimental weapon. Nothing worked though.
Any luck solving this?