Not having PDFs in Apple Books

Despite not wanting PDFs in my Apple Books library it has gone and done it anyway and I have thousands of pdfs clogging up the library view. The default setting for any PDF file is to open in Preview and has always been so. If I had a few days to spare I could delete all the PDFs in my Apple Books library but how can I be sure this is not deleting them completely when it says "Delete Everywhere"? I still need these PDFs but only in the original context in the Finder, not in my Books library. Also, how can I stop this happening again in the future?