Hey
Not sure if you fixed this issue already. I was having I think the same problem as you were, and when I disabled/unchecked the iBooks box for iCloud syncing on my device (iPad Air) and on Macbook System Preferences, I was able to get my books to show up on iTunes again. I just also updated iTunes and iPad softwares. I did the following after what this article stated https://tidbits.com/article/16378
On the Mac, in System Preferences > iCloud > iCloud Drive Options, uncheck iBooks
On iOS, Settings > iCloud > iCloud Drive, switch off iBooks
When I did that, all the books that were originally missing in the iTunes sync window were now also gone from the iBooks app on the Mac. So if you don't have the original epub files for some reason, then maybe don't try this. So I just went back into my finder and reopened all my pub files with iBooks, and the books I re-added to iBooks were now showing up in iTunes.
Sorry if that was confusing, but hope it helps. If not, really sorry and hope you find/found another way. I have been trying to figure out how to get my non-purchased books to show up on iTunes for weeks.