To play SOS again you need to start each of the objectives again. So in addition to "CLU", "Zuse", and "Light Cycle", you will need to start Quorra,GEM,Flynn,Discs mb, recognizer and TRON. Then the scoop will be lit for SOS again.
Quoted from NightTrain:So I was playing Tron last night and I got to SOS. I started it and I had "CLU", "Zuse", and "Light Cycle" flashing still. So i finished CLU and then drained before I could finish "Zuse". I started ball 2 (extra ball) and completed Zuse and Light cylcle. Then I hit the arcade scoop and SOS did not start again. Am I missing something here? I could have sworn you could play SOS more than once. Do I have to complete something else before I can start SOS again. Or can you only play SOS once per game, and then you need to light them all solid after that to start Portal?