Ummm .... No, he didn't ... he was significantly smaller than how massive he was at THE START of filming for Batman Begins, but that's it. Bale himself wasn't the same size all through out the filming of Batman Begins. He lost alot of weight during filming for a multitude of reasons.
Technically yeah he was smaller than he was in BEGINS, but most of the scenes he actually filmed in the bat-suit late in filming, that size he was is the same size he was at the start of TDK, and by the end of TDK filming.
He was continuing to lose weight all throught out filming till they got him down to the weight they wanted him to be at.
In most of the exterior scenes filmed in BEGINS when he was still losing weight, sweating his ass off in humid Chicago summer in a tight rubber suit, he lost alot of weight.
Having met him twice during both filming sessions, he was the same size physically in TDK as he was by the end of Batman Begins. He didn't lose alot of weight.