I've had this problem for some time. I think updating any of my devices causes iBooks to make my recently saved PDFs vanish across all devices. Yet much older PDFs remain synced across all devices. Its like it doesn't like certain versions of PDF after an update, and they vanish across all devices that are synced to the same iCloud account. I gave up re-downloading the PDFs (and just kept bookmarks in the browser) until I found a work around or Apple fixed it. But what I did discover was when I downloaded a PDF of interest I had previously had saved, it re-appered in the Collection I had created without me needing to move it. It's like it new it was the same file and new where it was previously stored.
Yes I tried signing in and out, and forced restart of iPhone 7+ etc., but the thing I think that triggered them to all magically reappear now was to toggle off both the "Sync Bookmarks and Notes" and "Sync Collections" then wait a minute, then toggle both on. Then after a few minutes all my PDFs appeared in the Collections on the device I did the toggling on. What's even more quirky about this, is I had the same issue on my iPad and Mac with them vanishing as well, as I sync iBooks across all my devices, yet magically on my iPad and Mac, all the collections reappeared once my iPhone had resynced and resolved itself. I'm not 100% certain it was just the toggling as I had previously tried loads of things from other searches and one of those could taken a while to kick in. But anyway, all my numerous PDFs are back in all their Collections.