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I thought about doing something like that, but I didn't want to have to do a bunch of experimentation for my first whistle design (single tone, as you mentioned).
But I have had issues like that while testing for a more recent design. If you squish it, you're gonna want to keep it printing on it's side (so it prints tall). You may need to experiment with also lengthening (or shortening) the body of the whistle depending on how much you squish and stretch to limit issues with changing the frequency shelves.
You can make simple stretches right within Cura! It's the second option on the left (Hotkey: S). Be sure to uncheck the "Uniform Scaling" box! Good luck! Let me know how it turns out!