How to remove the flavor from whisky stones?
To eliminate any off flavors that may have been absorbed, soak them in warm water for a few hours. Be sure the stones are covered by at least a couple of inches, so that there's plenty of volume to absorb flavors.  Agitate them every now and again as well.

When you place them back in the freezer, be sure they're dry (any surface moisture will more readily absorb flavors) and keep them in a sealed bag or container.

For what it's worth, it sounds like your sub-par experience is similar to that of many whiskey nerds and my own.  There's really not much need for these things.  You can get a similar amount of chilling by using a thick-bottomed glass placed in the freezer for at least 15 minutes or so.