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Thread: JSF question
if you don't unpack that deed before dropping Imp and going rebel again, you may not be able to use the deed at all.
You won't lose your ships, but you will lose access to them, until you get the skillboxes back, pull anything you might want out of them..If you have an ARC do NOT re deed it. Those mission flags are bugged, and you wouldnt be able to unpack it again when you came back. Standard procedure lately has been for pilots to load out a Heavy Z95, then use that to regrind.
As for dropping, just talk to a recruiter, leaving the faction will also drop you as an Alliance Pilot at the same time. Remember to delegate/use all your faction up before you do.
So long as you have enough room for one ship, you will be fine. Imperial ships can't be retextured or painted, so having one as the number 4 or greater slot will have no affect, should you decide to fly of course. You only have to be Imperial on the ground, you do not have to do the follow-on mission Lord Vader gives you after rewarding you with the JSF. Of course, being the rebel scum that you are, I don't expect you to blow your own people into so much space dust.
So to answer your question, you will not lose them, you will just not be able to use them until you regain the requisite Alliance pilot skill to fly them.