I had the referenced message appear after a full shutdown when I had the persistant charging icon after unplugging. The SD card was working fine with books on it that I had been reading the same day, yet the message appeared and none of the books on the card showed in the library. I almost panicked and reformatted, but I did a full shut-down again, and the card and it's contents showed up again.
I hope this info can help someone, sometime.
