I believe going through the Rubicon does replace missing parts? In Spears of the Emperor it was used to rebuild the destroyed body of an Astartes Captain.
Marneus was indeed missing all 4 of his limbs, I suspect they are back now.
His body was cut up, it wasn't dismembered. He still had everything where it should be. It brought him back to being functional, it absolutely didn't regrow any missing limbs.