So for the book to be typeset, we have a glossary created with glossaries that contains the word Auflage. The fl ligature has to be broken up, because this is a morpheme boundary. So using babel and it's "| feature works throughout my document, but in the glossary, there is an issue, see my MWE:
\documentclass{article}
\usepackage[ngerman]{babel}
\usepackage{glossaries}
\makeglossaries
\newacronym{Auflage}{A.}{Auf"|lage}
\begin{document}
\gls{Auflage} vs. Auf"|lage
\printglossaries
\end{document}
And here is the visual result, where |" ends up in the PDF:


selnoligby @UlrikeFischer before, but short before delivery I want to stay withpdfLaTeX.LuaLaTeXcan be used for the next deployment. – TobiBS Jun 07 '20 at 18:32