Crap...
It seems the only solution is to backup all of my sideloaded books and do a complete factory reset of the device. This time, I will activate the My Notebooks feature first before restoring my stuff back to the device.
I thought that there might be an "auto-installation directory" where I can just put these zip files for the device to install during a reboot. This was a common technique for jailbreaking Apple devices.
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