@mikeywilliams25: I am confused. According to the debug log you sent me, you did not attempt to connect. Assuming that you really did attempt to connect, the only way I see where nothing would be in the log file is if one of the extensions in the "Formats and folders" setting points to a non-existent folder in main memory. I will add this case to CC's logging.
Having the private app folder work when other folders don't work also doesn't make much sense. By any chance are you running a non-standard Android system? Is your device rooted?
If you are willing to take the time, what happens if you delete the former book folder "/books" then use CC to move the storage folder back?
Regarding finding the books in the folder but not in the database, you can do that by connecting to calibre as a wireless device. CC will scan for books and try to match them with what is in calibre. This process is hit-and-miss because the metadata in the books can be wrong. You might find yourself needing to take the steps described in the FAQ
I have books calibre shows as "On Device" but not as "In Library". What do I do?. It is often easier to ensure that CC and calibre are in sync by deleting all the book files on the device (using a file manager) then resending them from calibre by connecting as a wireless device, searching for ondevice:true, selecting all, then sending the selected books to the device.