As of the start of this month all apps have to consider iPhone5 resolution. In other words you have to do something to fill the space so you can't just use letterbox mode as the black bars will result in a rejection. What you can do is change your project to the new iPhone size, keep everything centered at the old size you've already created it at and then create dummy graphics to fill the spaces.
The people with the older phone can still play your game. The idea is to develop the game so that it adapts to the different screen sizes, so if somebody play on an iPhone4 or below the game will still work as expected, and then when someone plays on an iPhone5 the game adapts to the larger screen area, either by filling in the spaces with static images or using rules to adjust the placement of actors depending on the screen size.
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I still can't get mine to work though! We need a tool @wayneh001 :P