Thanks for the explanatios.
I've also edited my post to clarify runners (hopefully with the correct terminology this time). I'm trying to switch from 'runner on _' to R1,2,3 as appropriate.
I actually saw the play I described back in 2006. The umpire ruled that when the defense obstructed one runner, all runners were then protected, so the out on R2 was nullified even though she was neither obstructed nor affected by R1's obstruction.