Um, did you really have to take the other games down, though? I know they're not really "down", but they are still great VNs that deserve some visibility. Couldn't you just update the READMEs and sites to have a notice about how the world has changed substantially in your latest game? There are lots of people (including me) who would (and do) love those games, while not being interested in this at all. Just a suggestion.
EDIT: Or maybe put some kind of splash screen that has a disclaimer, I don't know. All, I know is, I've seen people retcon certain things about their game worlds before, and they almost never just outright remove their previous games from public view.