When it comes to reffing weather moves in regards to clones, yes, generally I ref the clones as disappearing if Rain Dance, Sandstorm, or Hail is in effect.
But most Pokemon have a way to find the real Pokemon among its Double Team clones. If you look up your Pokemon's moves on a website like Psypokes, and check the movelist topic, you should be able to find a way through.
As for switching out, yes, I can allow that, but it's like Baton Pass; you have to bring it back out later on. It's just that with doing a regular recall, any stat changes are lost if you don't use Baton Pass.