You've run into the problem of the Nook disk split personality. There are basically two separate storage areas, one for the books you download wirelessly from B&N, and the other for the books you manually copy to it using the USB cable, what they call "sideloading". The sideloading area includes any SD card you may have. Your sideloading disk space is wide open, but your B&N download space is just about full. What many people do is to download their older books to their PC and sideload them to the Nook, then archive them which removes them from the main download memory. Or you can just archive the older books. They will be available to unarchive and re-download should you want to re-read them later.
They will be available to unarchive and re-download should you want to re-read them later.
They *MAY* be available to re-download later. It's rare, but sometimes the publisher transfers the rights back to the author, is found to be in breach of contract for a mistake, or is redoing the ebook (creating a new ebook edition) and the book isn't available to re-download. So if you choose not to sideload, make sure to still back up all your books on your computer (via Nook for PC or NookStudy) before archiving. That way if you can't re-download for some reason, you have a backup copy that you can sideload.