If Link has the flippers, and the rule 'Link Drowns In Walkable Water' is checked, he will get stuck in dry lakes (which appear on screens with the 'Whistle->Dry Lake' checked, after he plays the whistle), whether they started off walkable or non-walkable.
Also, he drowns in what starts off non-walkable before the whistle is played if he does not have the flippers. I'm not sure if drowning in dry lakes is a bug (whether they started off walkable or not).
Here's the test quest file: http://www.freewebs.com/masterpikachu/ZC%20Content/Test/quicktest2.qst
NOTE: Play the whistle and enter both types of water before you get the flippers, then pick up the flippers, and try entering the water again.