If a [gear] token is on a ship that's obsoleted and you don't choose it as one of the up to two [gear/pilots] you can immediately repurchase, is the token removed from the game forever?
Yes (although the number of supplied gear tokens is not a game limit).
Do you put the associated gear *card* back into the discard pile for the market?
Same question for pilots - if you choose not to keep one, is it removed from the game [...]?
[Are destination cards reshuffled when the deck is exhausted?]