[ldolse]

Based on her responses either she's using Calibre's viewer to view pdfs, or she did a pdf->pdf conversion. I can't think of any other possibility (edit, saw Dwanthy's import theory, also valid).

Based on her insistence that it's any pdf viewer that shows them messed up the only explanation I can see is that she somehow did a pdf->pdf bulk conversion... Definitely a bad idea, and Calibre wouldn't do this by default, you'd need to go out of your way to configure a conversion like that. If the original files are deleted/gone there's nothing to be done.

Manichean's open question -- being absolutely certain you opened the correct file in the correct viewer -- is the only avenue left. The steps to do this, to be clear, are to find the book in Calibre's library view. Right-click the book, select 'Open Containing Folder'. Then right-click the file with the .pdf file extension, select 'Open With' (this may require holding down the shift key while right clicking), and choose a real PDF viewer, such as Adobe's own Acrobat viewer.

There other simpler ways to get the file open generally speaking, but they all rely on correct configuration of Calibre/your operating system. Following those steps should reduce confusion.