In LaTeX, the \includeonly statement exists to selectively add or exclude sub-documents.
One quirk in the whole process is that when sections are excluded, LaTeX decides to insert a page-break. The article at To have no pagebreak after \include in LaTeX recommends using newclude to avoid this issue. This package defines \include* which provides a work-around by omitting the implied \clearpage.
I am occasionally seeing the behaviour where if I comment out lines of my \includeonly statement the sub-document still gets included. Has anyone else seen this behaviour?
For whatever reason, everything is now working as it should.
Just in case the order of the \usepackage directives is important, in the working version \usepackage{newclude} is the first command after \documentclass{article}.