If the water is hot enough it is impossible for it to go into the ball...if this was a problem I'm sure the DynoThane president wouldn't be recommending such a cleaning method for all of their balls (especially the Soaker covers).
Have cleaned several balls using this technique and have yet to see any problems. Much better/safer than oven or dishwasher method to my mind.
Just make sure the finger and thumbholes are sealed...everything else is gravy
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Kyle: Chef, we need Butters to gain about 50 pounds, fast.
Chef: Well, if you want him to get really fat as fast as possible, one of you will have to marry him.
Stan: Marry him?
Chef: It definitely worked for every woman I've ever met.