I wouldn't mention the Jason version, except perhaps in a behind the scenes section. However, let's say that in Just War Benny reminds Jason about the time that he had cheated on her with a Zygon, in a scene that included the Doctor in the original novel (with no mentions of Zygon-cheating). I would still consider this fact to be a valid part of Benny and Jason's (and Zygon) history, as it's just dialogue about past events that took place regardless of the actual plot of Just War.