They don't need a reason to have characters in the game. Just don't have them in the story. If somebody asks "why is Sophie in SCVI even though she's dead" Bamco could just say "she's non-canon, just in it because we wanted her to be in" and be done with it.
Reminds me of E3 last year when a Bamco fighter was set to be announced and somebody told me it had to be SCVI because the DBZ fighter had just come out (Xenoverse at the time) and there can't be a new one announced. Lo and behold, Xenoverse 2 is out now yet SoulCalibur is nowhere to be found still.