Came across this situation in my game tonight: trying to remove a weapon system to add hard points to a ship is unavailable in the character builder.
I wanted to put a Light Tractor Beam on my Y-Wing and was willing to remove the Twin Light Laser Cannons to do it. This should have freed up one of the HP used by the current weapons systems and, in combination with the existing HP on the ship, would allow installation of the External Oversize Weapon Mount attachment (which would then allow the Light Tractor Beam).
Would this functionality be able to be added to the character builder or is it something I'd have to do with the data editor?
have you tried upgrading those with a tractor beam? might work that way.
Tractor beams (even the smallest - Light) require silhouette 4 and a Y-Wing is a silhouette 3 fighter.
If you can't do it due to silhouette restrictions why would you think removing the guns should be able to bypass the restriction due to silhouette size?