Since the Vanguard storyline deals specifically with a fracture in the timeline and includes that the MBL does NOT exist in the timestream created by Mxy, my assumption would be that the New MBL is in the Core Timeline of the HR Universe, albeit a damaged core. In a perfectly continuous universe, I'd say the resolution to the Vanguard dilemma and ours would somehow tie-in to heal any chronal damage.
However, that defeats our purpose.
So, what can we do for this team? I'd say continue along the basis of the HR timeline, purposely leave certain things in the dark about the past year, consider certain characters to be temporarily removed from the timestream, and blame any hiccups on what's happened since we last saw the world (and eventually have a cool reveal of what's been going on once the stage is set). With luck, once the other half is returned to normal continuity, all will be meshable.
All else fails, we do what we've always done - blame cosmic forces!
I think we need to figure out what we want this team to be, then we can get folks to come join it. We can even have returnng characters if folks want it, old Vanguardians or HR MBL guys or the like who are in Pro's thread, and still keep it free of deep continuity.
