BrickLink shows that the 10225 R2 D2 set contains 3307 Arch 1 x 6 x 2 "Thick Top With Reinforced Underside", but I purchased that set and mine contains the newer "12939" variation which is described as "Thin Top without Reinforced Underside". Does anyone know which is the correct ORIGINAL arch variation contained in this set? And when did the change take place?
I cannot give you the definite answer, but LEGO changed the design of the "Brick, Arch 1 x 6 x 2" two times over the last 6 years. The original version is 3307 which was in production/circulation until 2014. It then produced 12939 which entered production/circulation in 2010 and is still out there in new sets, however, in 2014 LEGO started producing yet another design numbered 15254.
Since 10225 R2D2 was produced for about 2.5 years from 2012 to 2014, it fell right smack in the middle of the change-over between these 3 molds. So per set it really depended on what mold had been printed and was sitting in the supply for the given production facility - some sets will have gotten 3307, other sets 12939 and even some late sets will have gotten 15254. For LEGO there is no difference in these parts and they will have been substituted.
Bricklink indeed mentions 3307, but has 12939 listed as alternate, so it recognizes both came in this set. Brickset has both 12929 and 15254 as parts for this set, and Rebrickable has 3307. Finally, BrickOwl is missing this piece from its inventory altogether.