In the end, it would largely be up to you how it would make more sense to you to do. Obviously we can't know for sure without details, but from what you've described it sounds like your latter suggestion would be most feasible: you can app the earlier version and then canon update them to include all game memories as well as the AU. However, if you think it might be more interesting to play with the gap in memory, for example, that's fine too!

You can submit it all as one app, right away, too, and we can respond to the canon update information right off the bat, as well.

tl;dr your suggestion is most definitely possible, but it's mostly up to you how you want to do it!