In .92 I have seen a lot of Lowers getting eaten by the newer generation spawned with Adventure Tech so given time it will probably sort itself out.
As for the new recruits, I would assume you would have some new gear for them and as such they can become tougher easier than the first crews you meet/recruit early game.
Though having some fodder around to Level with would certainly make things a bit easier.
As to losing the new recruits, just arrange your stack so they are first or second in line as it seems the game eats stacks in the order their Icons are listed, death coming first to those on the right side...