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I was in my flgs today and finally got two starter boxes (following internet wisdom), I now want to know what do I actually need from the second set, it seems the main reason to get multiplies is for the cheaper ships, do I also need to keep any of the pilot cards etc?

Why would you get rid of anything? I think the extra dice are needed to help the game go quicker.

I'm thinking more about pilots etc, if I can make a few quid off unnecessary spares then that moves me closer to an expansion

You need everything. Lol. Keep it all. All skills, all extra pilots (even the named one) in case you and a friend want to play and each use the same pilot: one a clone or LMD or w/e and each seeks to eradicate the other to be the "true" character. Star Wars has both clones and LMDs, so it's a fair scenario. You won't ever use both, but friends will. Don't get rid of any of it.

Excuse my ignorance, what's an lmd?

Life Model Decoy. Nick Fury in the Marvel universe uses them a lot too (anytime he dies, it's an LMD). Guri, from Shadows of the Empire was essentially one too, but they gave it a different name. Been a while since I read it.

Ah yes I see, Iv read most of the eu stuff and didn't ring a bell, but I understand now

I just put away the second cards of unique pilots and upgrade Astromechs into a baggie since t hey cannot use more than one of them per game anyway.

I've sleeved the cards, but only one of each of the 'Unique' cards. The rest are stored in my extra starter box.
As far as a secondary market, there isn't much of one in the US for those unique pilots. Almost everyone who has the game has all of those pilots. Exceptions would be the alternate art cards that are sometimes handed out at tournaments, etc.