I'm not sure it's so much the Helium being deflated by the TSA so much as it is the air pressure changing (the way a plastic water bottle will deform during landing).
I've gotten to my destination with it both inflated and deflated without having a TSA inspection notice in my bag (and vice versa too).

That being said, there's still very good padding on the bag itself and have never felt nervous flying with it. But I also ensure I remove the bars and rear derailleur though.