I’ve just been through the same problem and resolved it quite easily.
Through iTunes Connect the app has to be in the state of ‘waiting for upload’. At first I thought ‘prepare for upload’ was sufficient but not so. Thus you need to go through the questions about have you changed encryption and how you want the new version released etc.
Once you’ve been through this section of Connect then the app is in the correct status of ‘waiting for upload.’ My validation of my app then just went straight through.