I would be very keen to know if you ever solved your problem?
I am having the exact same problem. Deleted file in iPhone/Keynote. It got deleted from iCloud and iPad.
Tried restoring from the iPad backup.
But to no avail. The document cannot be restored from the backup.
I find this extremley frustrating since we are not expected to rely upon TimeMachine for iOS therefore the iPad backup should recover these files.
https://m.youtube.com/watch?v=cVgpaZJVjoo this video helped my sister with resto ring all of her documents. After updating her iPad her pages suddenly said she had no documents. If you have them backed up in icloud you can restore them. I hope this helps, I know it's late but maybe it will help someone