PDF is a LAYOUT/paste-up format originally to allow users to print the same as every other user.
HOW it was made, affects the quality of conversion. PDF is not a Linear file like an EPUB (every item/entry in order of use. Start to finish).
What it contains (pictures or charts...), affects the quality of conversion.
So back to your Q. An EPUB created FROM HTML has a better chance of converting back because the source was linear (and probably has no ligatures)
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