The T-Boost and +-Boost bonus can carry over to a Mega match in some cases. It's only the Megas that recalculate their score that it doesn't work on. That means things like Diancie, Blaziken, Swampert, Sceptile always (I checked with Diancie and the game doesn't constantly recalculate as barriers are destroyed), and in rare cases things like Lopunny and Audino etc. if no other tiles are cleared. So it's the recalculation of the damage that determines that the bonus won't carry. On the same token, the bonus as Sleep Charm and Burn etc. are wearing off will likely still apply to a Mega match that doesn't recalculate.
Included in Megas that don't recalculate are all Megas whose effect fails, such as Steelix with no blocks, Aerodactyl with no r/b/c, Rayquaza if no other Pokes are removed, etc. Basically if the score for the Mega match is not changed after the first number appears. If that's the case then it will still be boosted at the end of Sleep Charm and as the match after activating T/+-Boost. I'm pretty sure that's it. If I discover anything else out of the ordinary, I'll let you know straight away.
From /u/Avengahm