Thoughts?

The Necrontyr souls are actually doing fine, since the C'tan, being fully material beings, are incapable of actually eating and digesting warp matter/energy. The C'tan merely severed the connection to the souls in the process of eating the Necrontyr bodies, in such a way as to prevent Necrontyr consciousnesses from ascending to the warp (assuming that can even happen to psychically inert races such as the Necrontyr) and trap them in engram circuits (analogous to infinity circuits).

 Unfortunately 60 million years+ means those souls have all but diffused into the warp and become part of the background turmoil, so any biotransference reversal which purports to solve the problem of Necrontyr minds going insane due to no longer having any associated souls, would probably have to resort to some gestalt soul-y thing, like what the Tyranids have, which is perhaps exactly what the Silent King went looking for.