In this case, a major transition cliff (rather than a smooth arch) in an early chapter tipped me off that something major was wrong.
I had written something that went there. Why wasn't it there? Where was it instead?
5400 words, or thereabouts, had vanished from the chapter. Interesting words. Plot-critical words. Exciting (I hope) ) words. Words that not only did something right there at that moment, but set up things later, in terms of character, motivation, etc.
Where it was, was in the very long piece I had cut up in chunks....only somehow I had put chunk 4 after chunk 1, instead of chunks 2 and 3 (this isn't precise but it will do.)
I hadn't seen it in the onscreen version because...because sometimes you're just too familiar with the flow and slide over gaps when you're looking at the version you're most familiar with (to me, that was the onscreen version.) In print it was obvious. Thank goodness, because an editor would have catfits (mountainlion fits) at something like that.
It's also a great relief because I knew the word count was too short for the amount of plot I knew I had...I thought I'd lost my ability to connect plot-size/complexity to wordage, but no, I'd just left out a chunk.
So instead of an evening of catching up on email and playing around with images...I've been fixing it. It's fixed (this one--I wonder if there are others...) and I'm going to bed before midnight. I am not a night-owl...and I've been up well after midnight working on this thing for too many nights.
Always let another pair of eyes roam over that ms. before you send it out, and always see it in more than one format.