Kharnete did some tests and these are his findings:
Tested it. The first few times I had God Mode On so I could do it quickly without worrying on the survival part, but there was no way to damage the shield generators. And as you say, the Executor always starts at 50% shields.
After several attempts I turned off the God Mode, because why not... and suddenly I was able to destroy the generators (although I died with the Executor ramming me once the mission was completed, lol). Closed and started the game to try again, and it was still working. On these last both cases the 50% shield thing was still there.
So I'm not sure. Or either it was just luck and what solved it was the multiple mission restarts, or the God Mode has something on this. Which would be weird as hell, as I suppose you aren't using it... and either in that case, the God Mode is supposed to protect you, not your enemies, lol.
If it serves, I was flying it from the simulator, not using a pilot on that mission. It shouldn't affect this, tho, but I've seen other XWAUpgrade issues with different results depending if you were on the Sim or on the Campaign.