Short answer to that is "No"
It will definitely not affect any encysted stages, which are of most concern.
Free stages and eggs may or may not be affected, depending on the dip.
But since the corals usually start to slime like crazy and you transfer them kind of "dry", the likelihood of free stages hitching a ride is rather low. This may eliminate parasites without a cyst stage (Brooklynella for example), but not Cryptocaryon or Amyloodinium.
Uronema as a scavenger on dead tissue and bacteria may or may not be flushed off