Say I have a ditto active and my opponent has a fossil magmar, he
smokescreens my ditto. Then when it is my turn I gust of wind out his promo
mewtwo. Would I have to flip to do psyburn or would I not have to because I
changed into mewtwo.
The properties of Smokescreen stay with Ditto regardless of a change in the active. Just like Poison or any other Status effect, Smokescreen will not go away just because Ditto transforms.