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Thank you for the answers.
@DaleDe: I didn't post edit the pdfs. Most of them probably came out of some latex compiler and were not post-edited either. I don't use pdf reflow (and the problem persist even with zoom=100%).
@dwig: it's a bit strange, as the characters are actually showing, but in the wrong places, but still seems a reasonable explanation. Can you recommend a (linux) tool that does that? (I have found some examples with pdftk and gs). By the way, do you know the way to find which font would be missing?
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