While I had access to the SD card via Calibre I sorted out the books on my kobo into two sets, the add, read and delete are now on the device storage, the stay permanently on the kobo are on the SD card. They are tagged suitably on Calibre so if Calibre doesn't see my SD card it's not such a problem. I still think my USB ports are flaky so it's just waiting and seeing what happens.
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