iBooks: Deleting pdfs

I want to clear out some old PDF files (recipes, docs, etc) that are on my iBooks app (Mac, iPad). I've backed up the PDFs to a new folder on iCloud for safe keeping. My question is, if I delete those PDFs from iBooks choosing "Everywhere" will it also delete the newly saved (duplicate) files stored in folders on iCloud (that are in the Files app). They are quite large (and still important) files, but I want to tidy up my iPad. Will I delete them in both iBooks and in iCloud folders if I select "Everywhere"?

Many thanks for your clarification, as the Delete Warning's wording worried me a bit.