Smart...Very Smart Move
Direct one-stop through flights must clear both legs and the same seat must be open on both legs. Even then it's not a sure thing as operations will leave upgrades open for folks bording the second leg.
I had a recent flight booked as one flight with a stop over SAT-CVG-LGA. Inside the three day window, my upgrade did not clear. So I checked seat availabilty on line and was suprised at how open it was on both legs.
Called SMS and they explained that yes either leg is open but as a through connection it is not...go figure. Something about leaving some upgrades open for folks joining the flight later on. So I asked, if I bought a one-way SAT CVG in say LUT (I was on Q) and then a one-way CVG-LGA right now, would I automatically clear being inside the 72 hour window. The answer was YES but since I bought a direct flight the answer still was NO. I explained that this is most unfair as a FO in LUT could upgrade and here a GM in Q can't. Well after about 45 minutes, most of it on hold, I got them to clear my upgrade. Considering there was no difference in price for the two legs added together vs the direct flight (at least in my situation), I should have booked them individually.