Ah, the good ol' Time Cop problem. You might go for the One solution, and have the party meet new versions of NPCs they know and love. You might emphasize the comedic parts of this by going full Back to the Future, or you might just recycle everything and go for an undead BBEG that was killed early on in this setting, got moving again, and started up the plot of the time god again.

The problem is, you might cheapen the hard work of your players and the sense of accomplishment they had when taking out the BBEG. It's better to get a new BBEG, or perhaps even just conclude the campaign and create new characters in the new timeline. Sometimes, the story is over and everything just ... stops.

I think you need to ask your players. Do they want to explore the new-old setting with their characters, do they want to retire the characters and make new ones, or perhaps it is time to play a different system for a while? It is a nice opportunity to have a crowning achievement of sorts for a campaign, after all.

Maybe the players want to make the 'next generation' of heroes - their old heroes retired and started families, and now their sons and daughters want to go out and make a mark on the world.

And much the same is likely true for the villains that were thwarted or killed by the heroes - their sons and daughters are now of age, and can do something about the heroes and their heroic offspring...