Answering for Dominik, as that is easy to check by inspecting the PDF
file (the original one, obviously):
> I assume you have already considered: are the fonts embedded in the PDF?
Yes.
> Did he enter the characters as precomposed combinations or by using
> combining marks? First option more likely, I imagine.
Irrelevant, but you're right, it's the first option.
> This is a real shot in the dark, but here goes:
> Is it possible that, at some point in the process, the precomposed
> characters were decomposed and then put back together in a way that affected
> the output?
Possible in general, but that's not what happened here. The
problematic characters are coded in the PDF as single glyphs.
Best,
Arthur
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