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If a Ditto holding a Choice Scarf transforms in to a Mega Pokémon, will the effects of the Choice Scarf still take effect?

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Yes

Since you wanted proof of this, I tested it a few times on Showdown
Battle 1
Battle 2
Battle 3
Battle 4
Battle 5
Battle 6

Notice how Ditto went first every time
There is a 0.015625% chance that that would happen in a real match, assuming speed tie. So I think that's close enough.
You'll also notice how Charizard-X's Leftovers worked it if was already in that form. That implies that in the mechanics, if you have a Mega-evolved Pokemon (through the use of Transform and stuff) the other item it carries will take effect.

>Choice Scarf is the only item that allows it to effectively check set up sweepers and Mega Pokemon
Ditto can also be used to copy an opposing Mega Pokemon that threatens itself and attempt to sweep the opponent, such as Mega Pinsir or Mega Garchomp. Good use of this ability can let you overwhelm your opponent with both a copied Mega Pokemon as well as your own.

^ Kind of implies that Choice Scarf takes effect, since it lists Ditto as a good deterrent against setup sweepers (Smogon btw)

>The next turn you megaevolve and think you are going to start a sweep. In comes imposter ditto and now you are swept by a +3 attack scarfed mega pinsir

Somewhere
>Because Ditto can transform into a Mega Pokemon now, I've been running him to surpass the 1-Mega limit. It's pretty awesome stealing someone's Buffed up Mega Kangaskhan, knowing full well I've got another Mega still lined up, and Sucker Punching it with Choice Scarf.

Somewhere

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Thanks.
1 vote

Yes it will. Source-Bulbapedia

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"The user will transform into Mega-Evolved Pokémon and maintain the form regardless of whether it holds the required Mega Stone."
It's not clear wether the item still takes effect or not.