I hacked the NC with Autonooter 3.0 successfully and everything is running smoothly. But I have one concern. My BN reader can access all the old epubs that I sideloaded into the main memory before rooting the Nook. Now that I've rooted it, none of the file organizers can seem to see this memory but the BN reader can access and read any of the books I previously loaded. The new readers, like Aldiko and Adobe can't seem to get access to these books. Can someone explain this to me?

Should I be loading any future books onto the external SD card instead?

Thanks.