Coming late to the party, but I think this may be linked to a bug which I notified to the Frescobaldi team earlier this year:
https://github.com/wbsoft/frescobaldi/issues/646 <https://github.com/wbsoft/frescobaldi/issues/646> It happened when I reopened a Lilypond file after finding an error in the PDF file I’d printed off. I corrected the error, printed off a new PDF from the PDF viewer, and Saved and Closed the source (.ly) file. I later discovered that the PDF file with the error in it had not been overwritten, and was still faulty. It doesn’t look as if the github conversation on this reached a conclusion, so the bug’s probably still there. Michael
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