So, with X-Men #7, we know that Krakoa can grow X-Gene positive bodies for mutants depowered by M-Day.
gone.jpg
(Endangered Species, Chapter 4, New X-Men Vol 2 #40)
It had previously been stated that M-Day destroyed the genetic samples of the depowered mutants.
Did Sinister's system have a failsafe for this, or is this just an element being ignored for convenience?