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I had a very similar problem. I tried to use the sd card from my Kobo Touch in my Aura. I had no where near 3k books; more like 34.
The card worked on a Nook Touch and on a Kobo Touch. It would start to be read in the Aura and just freeze. I even gave up one evening and left it in that state and went to sleep. Next morning still frozen. Only solution was to pull the card and use the paperclip.
I gave up, bought a new card, created a "touch" library on Calibre and added the books to the library. It was then easy to transfer what I wanted to the new card on the Aura.
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