Hmm, I would imagine that body modification as you mention wouldn't carry onto DNA, so they wouldn't carry onto our forms. I remember in book 7, when they were fighting the controllers in open combat inside an office building or similar, Rachael was very wounded in one of her forms, and since DNA doesn't get affected by physical damage, when going back to a human she was unharmed, albeit very tired, so I would assume modification does the same.