Why can't batter's and catcher's boxes be repainted later in the game?

Interesting that you should mention that. This was a big issue a few years back when Maddux, Smoltz and Glavine played for the Braves and were consistently getting strike calls about 4 inches off the plate. It was argued that the catcher was set up well outside of the catcher's box. Umpires DO have the authority to demand the catcher's box, batter's box, or foul lines be re-chalked at any point in the game.