I've already spoken about the idea that Dark Force's existence (any Dark Force) isn't necessarily dependent on that of the Profound Darkness. But here's another way to possibly continue the story despite the root of all evil being defeated:
Time travel. I know it's cliche, but it definitely could work here, and it would be an interesting concept. Someone, at some point, discovers how to travel back in time, and a follower of evil prevents the death of the Profound Darkness one way or another (it wouldn't have to be just taking out Chaz and company, either. It could be something as simple as destroying the Aero Prism in AW 2100 or something, thus preventing Chaz from ever going to Rykros). I would prefer to see a change right at the very beginning of time, with the Profound Darkness getting an assist in defeating the Great Light). My choice for that someone would be a person who was aboard the Alisa III, perhaps Aron, who would have witnessed the effects of being transported through time and space, or perhaps one of his descendants.
This would obviously cause drastic problems with the space-time continuum, and the only way to keep the entire universe from imploding due to the corruption of events would be to go to the source and stop this from happening.