Deleting pdfs from iBooks?

I have Files HD on my iPad, and when I open a pdf in Files HD and hit the "Open In iBooks" button, it adds the pdf file to my iBooks app (as it should). My problem is that when I delete the pdf from iBooks, it appears to disappear, UNTIL I open another pdf from Files HD... then, every file I've viewed shows up again. How do I permanently remove them from the pdf bookshelf?
Thanks very much.
edit Opened iBooks without opening another file from Files HD, and it repopulated the pdf list again automatically.
Message was edited by: zzzoren

That works if you've loaded the pdf files from iTunes, but when you view them from Files HD it doesn't appear in iTunes when you sync, and it doesn't stay deleted when you delete it from iBooks.
The only way I was able to permanently delete the pdfs from iBooks was to uninstall Files HD from my iPad. Now that iBooks handles pdfs I don't really have a use for it anyway, but it was handy to have for transferring files around.

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