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.