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Well, I got home and was finally able to plug my Nook into my PC and my sideloaded files were actually still there. I ejected the device and according to Windows, it was fine to unplug but the Nook itself said that it was not properly unmounted and my files were corrupt.
I had it delete the files and was going to transfer them to the device again but then, it wouldn't mount on the PC when plugging it in at all.
Erased and Deregistered the device, logged back in, and everything seems to be working now so far *fingers crossed*
In short....letting the battery die must have corrupted my entire profile.
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