I wouldn't normally post this, but seems like every hunter in the game knows it even on 1.5k rating.
For those, who is still unaware: hunter's flare effect completely removes subterfuge and shadow dance buff, and shadow dance still remains to be usable (unlike stealth, for instance), so if you use it inside flare (your fault!) - the stack will be gone.
With subterfuge this interaction seems to be in place for pretty long time and it's as big of a problem as it is with shadow dance. Basically any hunter counters you so bad that you can't damage anyone in their team at all, unless you keep all the stacks of dance and use them only outside of flare, but let's be realistic - it won't stop hunters to save flare for your dances or use it as defensive CD when you are setting up CC chain /w burst.
I understand the design of flare to counter stealth mechanics, but it's more about revealing stealthed person, not making it the most op counter in the game to subtlety rogues by mitigating all their damage potential.
I've been trying to get through with this to Blizzard since beta - numerous bug reports via game interface and several tweets to @WarcraftDevs, but I'm being ignored.
Maybe if the awareness around this problem will be increased they will pay attention to this.
TL;DR: Hunter's flare fks up shadow dance and subterfuge. Report this to Blizz to bring their attention to the problem.