I don't have the same issue that you have but here is my story:
I transferred my SD Card from the my Glo to my Aura.
The Aura was able to process the books and list them in the library.
The only download side is while the shelves were created, none of the books were added to the shelves.
I ended up using calibre to delete all the books and readd the books back on the device.
It would been better off if I just reformatted the SD Card and have calibre add the books back on the Aura from scratch.