In theory any unlocks you use as a sub before going f2p should remain... However I don't think that actually works, you'd be better off waiting till your account become f2p.
Your 2 crew skills will get re-set and you'll have to start again, or maybe they'll just get locked out? (unlikely)
One option would be to remove two of your skills to guarentee which one it is that stays, for example, I'd keep the crafting skill (assuming you have a crafting skill), since the gathering skills can be leveled up quite quickly at little to no cost...
In the end what you do is up to you, a lot of information about f2p transitioning and its unlocks is quite sketchy