Maybe he was brought before they went to fight Lavos, but doesn't seem like it, considering the whole thing (bringing them to 1000 AD) was very likely planned after. It could still be, but considering how Doan just enters the gate without worrying about the new future, unless he already thought about it during the time spent before the parting.
And then, it also can't be the Doan of the new time line, since... well, I don't think Doan has a secured existence in it. Considering how the time line now has many more people, and living in a more spread manner, chances are Doan will not exist due to the bloodline now having a very high chance of going a different way than it did in the bad future. At the very least, Doan will not be recognizable due to different DNA and stuff.
Now, in the case it did went how it originally went, eh...
I think this may lead to a dead-end, actually.