If you are able to add the files to an SD card using a different ereader, through Calibre, the Nook should recognize them.
I used to have a Kobo touch, and I had side-loaded books on an SD card. When I sold it and bought a Nook STR, I popped the SD card in and all my books worked.
Dragging and dropping the files themselves to the SD card (outside of Calibre) will probably work as well. Nook just reads epub books as normal and as long as it can find them on the card it will probably organize them into the proper folders itself.
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