It would seem they are not, at least indirectly. All non-cosmetical changes are retained, as well as optional retextures for HK-50 and HK-51. Also you'll still be able to paint him back and forth, but he will lose his visual upgraides each time you choose to paint him in his original style (he'll revert to his "not repaired" version of skin).
They can coexist just fine if you decide not to repaint HK.