Yeah, me too, experienced a disastrous loss of a whole bunch of audio. After which I made this note in my mixing notebook:
MORE THAN ONE COMP ON ONE TRACK IS DANGEROUS! Since then, as alluded to above, I don't "flatten" or do anything to these lanes/tracks, but simply cobble them together to get the best overall take I can assemble, and send their output to an aux-track, and record it all as a new track. Simple. No Kablooey.