Proto Behe is just a matter of destroying him before he heals. I tried different strategies to find the fastest way to take him out without killing the Schrodingers first (to farm his crystal) but after some time came to find Com Com Rav X and focus fire on him is the best way. One Rav to build a little chain, two Coms to tear him apart. Got his crystal after maybe 10 kills. Annoying as hell since the only way to get a re spawn is by closing the gate and going through that whole puzzle again.
He has 1500 strength.
I'm pretty sure you could just quit the game without saving in order to avoid having to redo the entire area. Auto-save you say? Either turn off your console or quit to dashboard to do the hard quit without saving.