What happens when Boba Fett causes you to remove a card like Chardan Refit or the X/7 that would bring your squad point cost above max?

No; your squad value is set at the start of the game and does not change.

It's exactly the same thing that happens to every other card that's discarded. The total cost of your list doesn't change when your Prototype Pilot fires its Proton Rockets, so it doesn't change when you discard your Chardaan Refit, either.

Also, I'm pretty sure cards that give you extra upgrade slots like A-Wing Test Pilot don't cost you those slots if Fett take those out. That would essentially be taking out two cards at once.

Specifically, discarded cards are considered out of play for all purposes *except determining squad point cost*.

What happens when Boba Fett causes you to remove a card like Chardan Refit or the X/7 that would bring your squad point cost above max?

The same thing that would happen if he takes Punishing One off of a ship. The value of that ship remains unchanged.