I wrote my first 4 books in WordPerfect, and 2 of them were well over 100,000 words. However, I didn't have one all-inclusive file for those longer books. Not a file for each chapter either, but several for large sections. The other two (75,000 words for the mystery and 90,000 for the other romance) were in one big file.
I learned WordPerfect in my legal secretarying days and always thought you'd have to pry it from my cold, dead hands to part me from it. And I suppose that's still true as I still use it for everything non-book writing.
Anyway, my fourth book, 90,000-word romance, got unanimous beta reader feedback that the male character was just too hard. My romances have different scenes in hero/heroine POV, and to soften the guy, I wanted go through all scenes in his POV and wanted to have them contiguous so I could be sure to keep him consistent. Getting all those scenes into one file and then putting each back where it belonged in place of the original was a royal PITA.
Right after I finished struggling through that, there was a Scrivener discussion at That Other Place with users posting screen shots of how they used the program. Looking at those screen shots, I realized how relatively easy those revisions I'd struggled with would have been in Scrivener, how much easier moving anything in a draft around would be. So I tried Scriv and have used it ever since.
One problem I've had is that Scriv has encouraged me to move things around a lot since it's easy to do, and I was spending way too much time moving a scene from this chapter to that one. So for the novel I'm working on right now, I've stopped using the structure of chapter, scenes; chapter, scenes in Scriv. I started out with a single chapter as a folder and have all scenes within it. The theory is my scenes are already at the right level, so once the draft is done enough I'm no longer moving things around, I can put in more chapters and move scenes into them once instead of constantly fussing. Worst case it won't be that easy after all and I won't do it this way again.