It sounds to me like a bug in that software, something like a bad
regular expression that is catching too much text. FYI, I'm guessing the
"functional characters" are something like the "[=" and "=]" that seem
to surround these citations.

FWIW, as well, this sounds like a needlessly complicated system. Why not
just use a BibTeX editor, or have this program export a BibTeX file, and
use that for the references? If you ultimately need a file that has just
those references, then you can use the aux2bib program to make one.

Richard

Thank you for your reply, Richard. But switching to a different bibliography software isn't really an option since I would have to replace over 340 references in the text.

I'm now closer to understanding the problem. When I viewed the source code in LyX (the LaTeX code) I couldn't see that something in the way the files were coded had changed. I used Windows Editor to open the two .lyx files, the one before and the one after the compilation, and I noticed that the umlauts (I'm writing my paper in German) looked normal in the original file (e.g. "ö" and "ü") but in the new file they had been transformed into codes (e.g. "ö" and "ü"). Now LyX didn't seem to have any problems with the coded umlauts although they were different from the original file. But the ordinary looking ones that appeared in some of the references generated by Bibliographix caused the corresponding text passages to disappear in LyX. I googled "ö" and found out that it's UTF-8 code. But I don't know what to do with that information. Obviously, I can use the replace-function of the Editor to transform the umlauts into UTF-8 and I suspect that that's as close to a solution as I will get with this problem. But I wonder what caused it.

Peter

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