It'll definitely keep Trauma Savant if you use synthetic skin to heal the scar, not sure about AI chip.

My trauma savant can't have any of the modded implants installed, I was going to put in a brain stimulator and it didn't appear in the drop down list. I then installed it on another pawn successfully. Now I wanted to replace his Bionic arm with and advanced bionic arm and could not. Anyone else have this issue?

Replacing arms should be independent of brain stuff anyway, so I think that's some other mod causing a conflict. Maybe check if any of your other mods change Defs related to bodies or changes bionic arms.