Here's what I can see happening regarding Supercharged- Once it closes for HHN, that'll be the permanent closure. Work could be done in the main ride building while the queue is used for HHN, and once HHN ends, full work goes forward on both queue and ride + the San Fran area if we're still thinking Hill Valley/BttF.
And once the coaster opens, they could also have a "new" area and ride open simultaneously.