Sorry this took so long to get back to you; I have a lot of work to do and I don't have a whole lot of time to spare.
Personally I don't think this is too big of an issue. We probably need to adjust the rules in the future to prevent this sort of thing from happening in the first place, but for now I think we can be lenient on it. That being said, I still think something needs to be done. I don't really like the idea of handing either player the win flat out, since Halcyon "technically" cheated, while Tabuu didn't win.
What I think might be a good idea is to let Tabuu decide between two possibilities; either he and Halcyon have a rematch with Halcyon using the older version of the team, or Tabuu can just let Halcyon have the win. That way Tabuu can have a chance at getting a more fair chance at winning, or if he's not bothered by it, he can allow Halcyon to just take the victory. That's just my idea though. What do you think?