Similar issue here. I’m using Connect and it doesn’t show any of my subscriptions. However, if I click on my frontpage it does populate with my subscriptions. When I go to the website it does list my subscriptions. I don’t think you’ve lost them. They’re just hidden for some reason.
Not an HVAC tech, but where are your air returns located? I would agree that keeping the fan on will help mix the air in the house. Closing all the registers on the lower floor might stress the system, but you could close a few I’d wager and be safe.