Reading the previous posts, its looking like advice is being repeated and confusing you. The review team do not cater for giving advice to individuals, their job is dealing with reviews of our books.
OK lets go back to the beginning. First open a new folder, drag into this folder the .iba book file, the Ibooks file, the title image and the four screen shots, now include the .itmsp file.Rename the folder as the book title. Drag that folder into My Documents. Thats the housekeeping done and everything is in one place.
The revised book is not a version, because at this point, you do not have a published book.
Open the .itmsp file in your book folder and start the delivery process as you did originally. Input any information that was not retained, select the revised book in your new book folder, cover and screen shots etc through to the delivery screen and that should upload your book again.
I am assuming that you have been using the same .itmsp file and not creating a new one by publishing from iBA.
Remember, the files xxxxx.iba is your working file in the iBooks Author application. The file to upload is xxxxx.ibooks
Its advisable at this point to delete the ibooks file in your new work folder and Export a new version to that same folder.Now you know everything is new and OK.
Now you can start the delivery process...come back here and keep us advised of the results.