So, per the R2-D6 ruling (if you integrate R2-D6, you keep your associated EPT), I am guessing if you chopper your Renegade Refit, you still get the shield, but nothing else happens to your ship?

The only thing that Renegade Refit does for your ship is grant you an extra modification slot, and reduce the cost of both your pilot and EPT. Since we know that point values are only considered for a ship during squad creation, and for calculating final points (in which case the value of removed cards like missiles/bombs still count), Chopper may eat your Renegade Refit without any penalty whatsoever.

Yeah, there's a lot of precedent for this; that discarding a card which grants slots and changes costs has no actual effects.