I've been receiving this warning and for the past several hours (erh, something like 12 hours now). I've been trying to narrow down what's been causing it, but to no avail. I managed to cut down the project to ~1000 lines of code and still produce the warning, but I've tried cutting out tens of different things from that ~1000 lines, and so far, whatever I try to cut beyond that makes the warning go away, making it incredibly difficult to debug. There's also of course no line the warning points to and no visual indication in the document that something is wrong to point me in the right direction.
Here is a link to the actual project that produces the warning. So far I've managed to deduce that \includeonly{basics,apd}
reproduces the error, but if you remove either basics
or apd
here, the warning goes away. Furthermore, while I haven't tested ever two-chapter combination, it is the only two-chapter combination I have found that will reproduce the warning (and no chapter by itself will reproduce it).
I am also able to remove ~half the lines from either of these files to still retain the warning, but, besides the actual amount of code I'm removing, I don't see any pattern in the code that does and does not reproduce the warning. I've also been able to remove the title page, table of contents, references, and index, and still retain the warning.
I apologize for not being able to give any sort of MWE, but I really wasn't able to get it down much more than \includeonly{basics,apd}
even after hours and hours of experimenting. Hopefully at least someone has an idea as to what this error even means so that I have a better chance of debugging it?
(FWIW, the pdf backend I've been using is LuaLaTeX, though I've confirmed that pdfLaTeX produces the warning just the same (from the TeX Live 2016 distro). Perhaps it's also worth noting that Texmaker (my current IDE) does not report this warning and I have to go into the log file to find it.)