When deleting books or documents from Notebooks (iOS), they move the a Trash by default. It is easy to restore them from that trash again.

Notebooks¬†provides a couple of settings to control how long items should remain in the trash, and one of these options is to delete documents immediately. In this case there is no action or shortcut to restore them directly from within Notebooks. If you use any of Notebooks’ sync or backup options, you have a chance to restore a deleted document or book.

Dropbox with Automatic Sync
With this setup, deleting the document in Notebooks automatically removes it from Dropbox as well. So you open your Dropbox in a browser, navigate to the book that contained the deleted item and activate “show deleted items”. Now right-click the deleted item and select Restore. The next sync brings the document back into Notebooks.
Dropbox without Automatic Sync
The deleted item remains on Dropbox as long as you don’t trigger a sync from Notebooks. To make sure that the document in question is not deleted during the next sync, duplicate or rename it in Dropbox (from your computer or a browser). The next sync will import the renamed/copied version of the document.
As long as you don’t sync, the deleted document remains unchanged on the WebDAV server. To keep Notebooks from deleting it during the next sync, you can either duplicate or rename that document on the server, or you deactivate the setting Sync moves and deletes.
Finder or iTunes Backup
Finally, you can also restore books and documents from the latest backup you created from macOS Finder or from iTunes, either using an app like iExplorer or other so called iTunes backup extractors.
The basic principle of restoring documents with these apps is to extract Notebooks’ contents to a folder on your computer; in the exported folder, navigate to Documents/Notebooks and you will find all you documents and their accompanying system files.
Can I Restore a Deleted Document or Book?