Originally Posted by Robert Leach
I would think each flight would clear independently, which begs the question as to why you intentionally booked it this way in the first place? Was there a fare difference doing it this way?
This was booked this way because if it's booked as a direct, 1 stop, upgrades have to be available for both flights or you won't get any upgrades even if the upgrade is available for 1 of the flights. This is also true with seat assignments, the seat has to be available on both flights for you to be able to request it.
To answer the OP's question, I don't know if booking as 2 flights fixes the upgrade problem.