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You have got me.     I replaced the tire on my 2012 S once, but not the belt.  My recollection is that, while you can adjust the belt tension easily enough, I don't recall any way that the rear cogwheel could easily be moved more toward the wheel, or the front cogwheel moved closer to the motor.  Unless it is really tearing up the belt, I think I would just let it go.  I don't believe it will hurt anything.  But if your bike is still under warranty, you might have your dealer check it out.

I can help..

When i rencently installed the 2013 motor on my 2012 S, i had to modify the rear wheel a bit to match the alignment of the 2013 motor sproket. In fact i machined the rear wheel sproket seat my 100 mil to accomodate the alignment of teh rear sproket. I playes alot to keep alignment perfect!

I had  amisalignment at teh begining and snaped the belt!! at 8km from home!.. The angle diff between the two sproket was over 0.25 degree wich is the max tolerance according to Gates, the manufacture of these carbon belt. 64$ later and a new belt with proper alignment it is working like a charm!

 If your belt is too close to the rear sproket shoulder, then you can remove the motor sproket and remove one of the spacer behind it. this is about 1.5mm thick and there is 3 of these . Then your belt should be  1.5mm far from teh rear sproket shoulder.

Not long ago I had to play with my front sproket too.

I removed one spacer (it had only 2) and the belt still slightly touch the rear sprocket shoulder. I believe this is OK - better touching the shouldered side as moving to the other side.

If I roll the bike back the belt will change its position and has a 2mm distance from the shoulder. This wasn't before I removed the washer.
It makes me think the belt now don't get so much pressure to the shoulder as before