The whole "Evil Timeline" thing was (most likely) just some random thought of Abeds' rather than some real thing. And what we saw in the S4 Finale was just some fantasy of Jeffs', not Abed. So if they want to continue they can just have what was going on in Abeds' head compared to Jeff.
I used to be completely antisocial, play a lot of video games and post on Star Trek forums. Now I'm socially active, play a lot of video games and post on Star Trek forums. Real character growth is tangent to the center, not directly toward it.