Here's the update.
I restored the iPad, no problem erasing the content. When I attempted to restore from the backup I had just made, it failed repeatedly, saying the backup was corrupt. Looking at the iPad content via iTunes, it appeared to be present. But I could not access anything directly on the iPad. I kept getting the instruction to "Connect to iTunes", and then instruction to 'start over'. I would do so, it would appearing to copying, then a message that the backup had failed.
I had to sync the device as a new iPad to be able to use anything. I then had to manually reorganize all the apps. Fortunately I had used a desktop app called 'iMazing' by DigiDNA, a file management app. This app is able to access a backup of the device content and I could re-copy a very large number of text files back to the iPad, with the previous organization structure, back into Goodreader. This literally saved me hours of tedious file management. I'm not sure if iMazing actually keeps a separate backup, or just accesses specific components of the backup archive created by iTunes. In any event, it was a huge time saver.
Bottom line: once I had reconstructed the previous content on the device, the DND and Other sections had been restored to reasonable sizes. So the original goal was successfully accomplished. Too bad iTunes doesn't make this process easier, but at least the third party app was a success.