Something that has popped into my mind is that when Charlie is trying to get into contact with Heaven, she doesn't ask her dad for help. You know, something she did back in season 1 so she could get a direct meeting in Heaven.
In fact, the Heaven Embassy (which is the building that Charlie meets Adam for the first time) is just never utilized or even referenced after the first episode of this series. We just, see it gets destroyed when Heaven's gate comes crashing down from Vox's weapon blast. It's just kind of weird.