I haven't changed any pdf settings, nor do I see any settings that effect importing pdf's, or converting them as you mention. The only settings I see are line unwrapping on input (haven't touched it) and metadata stuff. All I am doing is adding them to the library, ie database, where no conversion should be happening until I say so.
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Unless you told Calibre to do a pdf->pdf conversion (a really horrible idea) it would never do anything to your original files - Calibre doesn't attempt to manipulate pdf in any way.
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Unfortunately, this is far from the truth. I tried it several times. Raw pdf is perfect, no problems. Go to calibre and add to library> open pdf from library> hardly legible. Calibre is changing
everything about my files.
It's too bad I didn't notice this until after I imported almost all of my 800 or so book library, which is now decimated. I've definitely closed the book on Calibre until this is resolved, as 80% or more of my books are trashed.