"No PDFs" in iBooks on ipad; i.e. PDFs don't persist in Library
By default, PDFs don't persist in the Books app. In the Files app, opening a PDF with Books will make the Books app open the PDF from its existing location.
To copy the PDF into the Books app, with the book open in the Books app, tap the Share button, then ‘Copy to Books’. This will duplicate the PDF into the Books app container.