Does your extra energy bar still work if you are playing a scene you have already mastered?

If you're talking about the extra energy bar that you receive when you activate a star booster, then yes. The energy (either 110 energy for the regular bar or 150 energy for the extended energy bar) can be used anywhere you like: mastered scenes, unmastered scenes, and competitions. But the booster's ability to fill stars twice as fast, will not apply in mastered scenes, since the stars are already filled.