No android auto and says "USB hubs are not supported " after updating from SYNC 3 Version 1 to Version 3.4`

Have you master reset?, I would assume yes.

If so, your only option at the moment is to get a proper hub to see if that changes things. You will find information here Media Hub, CarPlay Compatible - 2015-2020 Ford/Lincoln - SYNC 3

I know the title says those are for CP, but we had a few cases in which users only got AA to work after replacing the hub…

If that does not work and nothing else should be preventing android auto execution (bad cable, bad configuration on the phone and such things), then maybe your issue is skipping 2.2.17xxx, go which there’s no solution since you can’t go back to that build.