Yes, that's right, calibre is only registering the books loaded onto the SD card and registers them as loaded in the main memory. The books loaded onto the main memory are not registered as being on the device at all (but are in calibre). When I check in Finder, both the Kobo and the SD card appear as drives, but it looks like the Kobo is actually the SD card and vice versa (judging by the content).
I'll try popping the card and seeing what happens. I'll also check there's no calibre metadata file on the card itself (I suspect there might be) by loading the card in my card reader not in the Kobo. Why do I think I'll be doing another round of factory resets?
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