I'm writing my own question and answer here, because there are dozens of them on stackoverflow, and all have different answers, none of which worked for me.
So, it's been many months since the new iTunes Connect launched, and for a lot of people it's still impossible to reject your own binary so you can replace it, for example if you upload a binary, the status changes to "waiting for review" and then you realise you have a bug so want to upload a new binary.
For many people, there are just no buttons/links/anything on the screen that allows you to modify the binary.
I have my own answer which I'll post now, but it's a total hack, so if anyone else has a sure fire and cleaner way of dealing with this nightmare of a system that Apple has forced on us, please post!
EDIT
Sadly, this didn't work, the old build was released even though everything on iTunes Connect indicated the new one was up for review. More details in the comments throughout this post.
Here's how to get around the problem ...
Upload a new binary, to do this you need to change the build number .. in the plist, this is "Bundle version" NOT "Bundle versions string, short", although you can change that if you want also.
Since everything, and I mean everything, about the app submission process is f***** then you probably wont get confirmation from Organizer that the binary was submitted, but it probably was.
Wait a short time, log into iTunes Connect, go to your app, click on the "pre-release" tab, you should see your new binary in there, it may still say "processing", if so .. I would wait until that stage has completed before continuing.
NOW THE HACK
In the "Versions" tab, there should be a blue plus icon right beside the word "Build". For me, there wasn't.
USING CHROME: Go to the "Versions" tab and scroll down to build. Right click on build and choose "inspect element".
Expand the div with class "section" and then the h1 with class "ng-binding". In here you will see the word "Build", right below this is a link (a href), it has three classes in the html ... "addIcon ng-binding ng-hide". Double click here and you can edit. Delete ng-hide. BOOM, the plus icon will appear on the web-page, you can now click and choose your new build, then save.
What. A. Complete. Joke.
DISCLAIMER
My app is waiting for review, I cant guarantee that Apple wont turn around and approve the old binary, but everything I can see in iTunes Connect suggests that it's the newer binary that is waiting to be reviewed .. so I'm hopeful. I'll update once the review is complete.