I had this problem. I'll share my ride on the learning curve.
First, I couldn't find how to reject the binary but remembered seeing it earlier today in the iTunesConnect App. So using the App I rejected the binary.
If you "mouse over" the rejected binary under the "Build" section you'll notice that a red circle icon with a - (i.e. a delete button) appears. Tap on this and then hit the save button at the top of the screen. Submitted binary is now gone.
You should now get all the notifications for the app being in state "Prepare for Upload" (email, App notification etc).
Xcode organiser was still giving me "Redundant Binary". After a bit of research I now understand the difference between "Version" & "Build". Version is what iTunes displays and the user sees. Build is just the internal tracking number. I had both at 2.3.0, I changed build to 2.3.0.1 and re-Archive. Now it validates and I can upload the new binary and re-submit. Hope that helps others!