Kaiyล II Mark might know about S6 Mark, but S6 Mark has not been told what Kaiyล II Mark has done nor will do after their split by any SAoY personnel, to my knowledge.
When they split they had to buy out their contracts. Any decontaminating processes that command deems necessary for someone that leaves the army went down, unless otherwise stated by Mark's player.
I don't think it necessary to have concerns raised unless it's something that Mark's player wants, then I'd be open to discussing it as his character's GM. As it stands, he has a lot on his character's plate and a "spot of bother" could lead to stress neither player, GM, nor character need.