It makes the air inside expand and will stretch the plastic and make the ball bigger. If you keep heating, the ball will split and let the air out.
I once tried to fix a ball that was pushed in and so had a dent by boiling it until the dent popped out. The dent did pop out, but the ball was bigger than it was and did not bounce like it should-- maybe a child could get some use from it, but to me, it was useless.
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On Mythbusters from Discovery channel, baseballs kept in a humidor travelled less than those that were left out...
Under the same impact force, a solid golf ball will have a longer overall distance in warm weather than in cold weather. That's why there is a business for golf ball warmer.