If i have a full 100 pt squad with Chopper on a Renegade Refit X-wing... Can i use Chopper's ability to discard Renegade Refit even if that would raise my points now above the 100 pt game limit?

I feel like the answer is No, that points only matter at the time of placement. But i just wanted to make sure.

Short version: Yes you may use Chopper to eat Renegade Refit, and you suffer no penalties for doing so.

You're correct that points only matter during squad building, and after the game for scoring. During the game, it's irrelevant, so yes, Chopper can eat away, and you keep on flying as usual. As a matter of fact, you lose nothing if you discard it! The card itself only decreases the cost of your EPT, and allows one extra modification to be added, so it has no direct game impact. One notable fact: the loss of cards that grant an upgrade slot (due to certain critical damage cards, Boba Fett crew, etc) do NOT cause you to lose the slot they granted - they only function that way in the squad building phase. (The only exception to this is a crippled huge ship, but that's an entirely different matter).

Discarded upgrades are out of play for all.purposes except determining squad point value. The only upgrade chopper can't eat is chopper.

Hopefully this is a theoretical question. X-Wings are too action-dependent to use an action to regain a shield when they can take R2-D2. And they’re too dependent on EPTs and mods to discard them and still be effective ships. I suppose you could slap one on a rookie, but I’d stick with R2 astromech or FAA.