AQW is a merge of all 3 timelines, but the creation of the AQWorlds universe did not destroy the other 3 games. When the sands from the AQ/DF/MQ hourglasses in the Dragon of Time's heart-chamber mixed, so too did all the people, places, and creatures of the original three games, and those mixed sands created AQWorlds.
We've got a fun situation with AQWorlds' storyline.
Inside the game, AQW's existence is NOW a mixture of the AQ, DF, MQ timelines. But as the cutscenes showed, the physical planet AQW is on existed before the merge at the same time AQ, DF, and MQ existed. (That is how the world could be destroyed, compelling Galanoth to slay the Dragon of Time and bring his loved ones back.) After the Dragon's death, new elements were introduced into the AQW world from AQ, DF, and MQ as you've seen throughout the Chaos storyline.
Outside of the game, you guys know and love AQ, DF, and MQ and see them updating alongside AQWorlds each week. AQW's canon does not necessarily determine the future of AQ, DF, and MQ's storylines, as each game has writers who wish to take their games in directions which may differ from what AQW does.
It requires a bit of a disconnect to wrap our minds around the fact that in the game, AQW blends together AQ, DF, and MQ. In reality, that isn't necessarily true.
Regarding Drakath in DF: Geopetal said she has no plans to touch on the Chaos storyline in DF, so it's not very likely you'll see a Chaotic Drakath appear in DragonFable.
Okay. This is by far the biggest thing bugging me here. When the Finale was originally revealed, people assumed that this was indeed what will lead to the whole AQW storyline, and frankly, people were angry over it. Sometime later, we had the Birthday event in AQW where we saw something completely contradicting this, a "seed of chaos" planted to Drakath's heart after the kidnapping by The Collector. It was a very boring night, so I made an incredibly convoluted theory that was supposed to somehow prove something via logic that made no sense. I even felt the need to make a thread over this. To my surprise, coming back to it the next morning, there were replies by, I believe, Alina and Geo, at least.
This will be explained before the AQW main storyline ends. I can't wait until this reveal; it is too much fun!