R2-D6 let's your Red Squadron Pilot have an EPT.
Integrated Astromech let's you discard your astromech to prevent a damagecard.
If you do use the ability of the integrated adtromech you lose R2-D6, does that mean you lose your EPT as well?
R2-D6 and integrated astromech
Try following this thread.
https://community.fantasyflightgames.com/topic/187953-loosing-an-icon-from-your-upgrade-bar/
The precedent from Epic is that if you lose a slot, you lose the upgrades in it.
The precedent from Epic is that if you lose a slot, you lose the upgrades in it.
Except it isn't a precedent as that is an Epic-play specific rule applying to Huge ships, and the Epic rules are separate from Standard-play.
Until FFQ release a FAQ on the matter there are no rules governing the loss of a slot in the middle of play so just carry on playing and having fun 
Aside from Epic play has there ever been a way for a ship to lose an upgrade slot before? Ok, I guess we do have on Imperial guy who will chuck other crewmen out the door but have any of them granted a new slot first?
Epic did set a precedent but now it needs to be expanded to the rest of the game as well.