I wasn't able to reproduce it by reconstructing new documents, so I started removing things from the broken document. It turned out that removing the bibliography at the end of the master document and re-inserting a new one solved the problem. I have copied the tail end of the before and after files to see the small difference. I will post these to the bug 11381 I created. Here is the diff.
$ diff before.txt after.txt 21c21 < options "bibtotoc,plain" --- > options "unsrt" Eric On Mon, 2018-11-19 at 11:30 -0500, Richard Kimberly Heck wrote: > On 11/18/18 10:47 PM, Majzoub, Eric wrote: > > Hello, > > > > I'm not sure if this is a LyX bug or if I'm not using 'include' documents > > correctly. I have attached a screen shot. The document has about 10 > > sections. > > Two of the sections are stand alone .lyx files that I have 'included' in > > the > > master document. The first stand alone section has its own reference > > section > > in a branch that I have turned off (so it doesn't conflict with the master > > document reference section). When I go to navigate it shows only the first > > section heading, and then the branch that is deactivated. When mousing > > over > > the deactivated branch it shows the rest of the navigation headings. Have > > I > > done something wrong, or is this a bug? > > It looks like a bug. Do you think you could produce a small set of test > files that show this problem, create a bug report at www.lyx.org/trac/, > and attach those files? > > Riki > >
