I had books that I sideloaded to my SD card on the NC and then put into shelves that I created, but it seems that every time I sideload new books to the SD card, all the books that I have added to the shelves disappear and I have to add them back to the shelves. I ended up taking them off the SD card and putting them back onto the NC directly so I wouldn't have to keep re-shelving them. Is there something I'm missing when I put them into shelves or are sideloaded book to the SD not able to be shelved.
Having the books that are on the SD cards "fall off" the shelves they were placed on is a known problem with the NC. Usually happening when the NC turns off and back on, but also at other times (like you have found). The only solution I have found is keeping them on the NC itself and storing my pictures and movies on the SD card. I hope this helps (but probably not by much) sorry.