Same for me with LOTR vs. Two Towers, and have e-mailed BN. I'm not optimistic based on other folks with the same problem, but will provide an update if anything happens.
Maybe folks could post any other "mis-transfers" on this thread. I, for one, have a LOT of books that transferred over, and it will take me a long time to open each one to see if it's what it purports to be, and/or to match them up and see if anything's missing or wrong. I'm doing a few a day, but don't have time to do a lot, so would love to hear about any others to check first
Like most of the rest of us, I do have them all backed up, but mostly in FW's ereader format, so would like to have the BN epubs, since they offered to do it....