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I think i got this fixed.....
I uploaded the book, the way that was working but not being displayed.... (see my post above)..... then I closed Calibre, disconnected the kobo device and then rebooted it.
Once rebooted (the books are still not showing) I connected the device to the PC again, and manually, through explorer, deleted the file KoboReader.sqlite. Then I disconnected and rebooted the device.
This was as if I just opened it from the box... it asked all the startup questions, what language I wanted, my wifi password, link to my kobo account etc etc....
... but once the device got to the homepage, the books I uploaded (that couldn't be seen before) could now be seen. Also, from now on I could upload, delete and edit metadata as expected via Calibre.
So, that is who I got it all working... I "think" the problem was as there were liturgically no books on the device the reader had not "created" a database of any kind... forcing the restart of the setup process by deleting the file, as it found books during this time, built the database. So now it can update and have things loaded in and out of it, as expected.
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