So, it turned out when I copied everything into a new folder to restructure the monograph, I missed a chapter. Realised a couple of weeks ago and had to restructure it again to fit in the missing material. Anyway, done now, and hopefully better for it.
Good grief, I think I might have finished a full first draft of my monograph! Not a good draft, obviously, but one that starts, has a middle and continues to some sort of end.