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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.
It does have the ability to create a pdf though using conversion, which is why converting to pdf->pdf would be a really bad idea, as it would overwrite your good pdf with a much poorer version. Maybe you accidentally converted all your old pdfs to Calibre created pdfs?
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