You can create as many directories on the device as you want. The only reason there could be an issue is if the total path for the filename goes beyond 260 characters. And don't put it inside the ".kobo" directory.
When you put new books on the device and disconnect, the books get processed and details are put into the internal database. While doing this, the device displays a black processing screen and counts up the percentage processed. Did this get displayed?
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