Hello, Covref!
I can understand wanting to recover your PDFs. If they were added to iBooks with the recent changes to iOS, then you may find them in iCloud Drive.
Use iBooks with PDF documents on your iPhone, iPad, or iPod touch
Sync and save PDFs
The first time that you open iBooks after you update to iOS 9.3 or OS X 10.11.4, you'll be prompted to use iCloud. Learn more about syncing your books and PDFs using iCloud.
Use iCloud Drive or iBooks to access your PDF files, ePub files, and books
You can use iBooks and iCloud Drive to sync ePub, iBooks Author books, and PDF files so that you can access them on all of your devices. After you turn on iCloud Drive, all files automatically upload to iCloud*. Any ePub, iBooks Author book, or PDF file that you add to your iBooks library later also automatically upload to iCloud*.
If they were uploaded to iCloud Drive, you should be able to restore them from there with this article: iCloud: Use iCloud Drive on iCloud.com, specifically:
Download files
You can download files that you want to copy from iCloud Drive to your computer. Any changes you make to a downloaded file appear only on your computer unless you subsequently upload the file to iCloud Drive.
-
Go to iCloud Drive on iCloud.com.
-
Select the files you want to download, then click the Download button
in the iCloud Drive toolbar.
The files are saved in the Downloads folder on your computer (or other folder specified in your web browser’s preference or option settings).
If the files are not showing in iCloud Drive on the website, double check to see if they might have been deleted:
Restore deleted files
You can restore files you deleted from iCloud Drive in the last 30 days, whether you deleted them on iCloud.com, your iOS device, your Mac, or your Windows computer. However, you can’t restore files you permanently removed as described in “Remove deleted files immediately,” below.
-
Go to Settings on iCloud.com, then click Restore Files (in the Advanced section).
-
Select each file you want to restore, or select Select All.
If a file was in a folder when you deleted it, the folder location is shown below the filename.
The list of deleted files may contain more files than can be shown at once. Scroll to see more.
-
Click Restore.
Look for your restored files in the folders they were in when you deleted them. For example, if a file was in the Pages folder when you deleted it, look for the restored file in the Pages folder.
Hope these steps help! Cheers!