What buttons does calibre show for the device? Does it show the two for the main memory and SD card, or just one? And in the device lists, does it have the correct books shown?
In the log, it only shows "/Volumes/KOBOeReader/". In Finder, is this showing the SD card books and directories? If it is the SD card, there will be a directory something like "koboExtraStorage" (I know that's not the correct name but, it's something like that). The main memory will have ".kobo" and "Digital Editions".
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