I sideloaded a couple of ePubs yesterday then placed them in a custom shelf. Later I modified both ePubs in calibre so they would look better on the NOOKcolor, deleted the original copies from the NOOKcolor, then copied the modified ones over. I did all the deleting and adding of files via a PC connection. I changed the filenames slightly. After I disconnected from the PC the original ePubs were still showing in the custom shelf even though I deleted the files. I never could get them out of the custom shelf. I finally had to delete the custom shelf itself to get rid of them, re-create the custom shelf then add the newly modified ePubs. Everything works, but the file system seems kluge to say the least.

Also, I cannot add ePubs from the SD card to a custom shelf nor copy them to internal memory using the NOOKcolor, even though the User Guide states you can.