The freshwater dip wouldn't have hurt the mushrooms. It may have hurt the bacteria on your rocks, depending on how long you left them in the fresh water. Fresh water dipping live rock isn't a good solution -- it would have been better to use the Flatworm Exit. Doing a freshwater dip on rocks will kill lots of good things on them, in addition to the flatworms. At least the Flatworm Exit only kills its intended targets. ;)