My Books app in my ipad pro deletes/disappears my pdfs. I am on IOS 12.2 and it is was updated a couple weeks back without issue
I've had the same problem. One of my friends gave me a slew of books in ePub and PDF format. Most of them are crap, but a few I really hoped to read. The only thing that has saved me is that I have iCloud backups of my iPad Pro. 

I've also been able to recover a few by syncing with my Mac, then opening Books and going to Collections->PDFs. Then I had to manually get them back onto my iPad Pro. 



Whoa! Suddenly they all are there. I re-authenticated on my Mac (entered my iCloud password) and everything popped up.

I don't know if we have the same issue, but it just might work for you too. Try logging out of and back into iCloud!