Basically as the author, you're God and can do what you want.
If you want to pick one path as the "official" ending to start the sequel from, just go ahead and do it. They do it in video games all the time.
There was a CoG thread bitching about this once and they all sounded like a bunch of entitled faggots saying "Oh well the author shouldn't make a sequel if they aren't going to account for every possibility. That's just lazy, because my character did this, blah blah blah..."
It's like fuck you, I'll do what the fuck I want. Besides, in the scheme of things, it doesn't really invalidate the other endings anyway. I've personally said on multiple occasions, a reader is perfectly able to consider ANY ending to be their own "winning ending" if they like it better than any official epilogue or whatever.
Every branch is a possibility since it's an imaginary story anyway. All of them AND none of them are what "really happened." You're just continuing the tale that you found the most interesting to explore.