Like Sliders?
Can I play?
Seriously though, Here's what I'd do.
You have your NPC entry for the character in question. We'll call him the Cabbie.
First game, you have Cabbie Earth Prime, he's inputted normally, nothing special about him. Let's use his description as the example. Here's how I'd put it in:
Earth Prime
This cabbie smells like hot dogs and speaks in a Russian accent.
The players meet him, and you reveal the description.
The next game, your players take a cab and you reveal the SAME information, but this time, there's a second, separate, description:
Earth 2
This cabbie smells like cheese and speaks in a Southern accent.
Reveal this as well once they meet him. They now see the first and the second descriptions.
Third game:
Earth 3
This cabbie smells like a hospital and speaks in a British accent.
Again, reveal.
You now have different "characters" that are the exact same guy, but have different descriptions. You can keep track, so you remember that you need a british voice for your cabbie one game and a russian one in another. Your players can keep track of who they've met using these bolded titles and different descriptions. With the player edition, they can have all the fun of tracking just how many cabs they've taken and marvel at how it's the same driver each time, and laugh at the differences and how they go with your world.
You can even do this for stats or character sheets for your own use. Cabbie Prime has his stat block all nice and formatted. You need to change some things out, because in Earth 52 he's driving a limo, so you copy the block, and paste it into a new snippet with the title
Earth 52 at the top. Change out driving skill (cabs) 3 ability with driving skill (limo) 3, add a finance knowledge skill, or maybe some fighting skills (he's a bodyguard in Earth 52, why not) and save it. Your players don't have to see that, but you can.
You can do this for each entry you change around, even with smart images.
Say you have a house and a smart image for Earth 3. Put it in, do your work. The label next to the tag is Earth 3. Add ANOTHER separate smart image, label it Earth 35, have its layout be slightly different. If you're linking rooms, have a separate container for Earth 35 from Earth 3, copy the contents of Earth 3, change what you need to change and BAM! Different universes.
Don't make it too complex, you'll go nuts keeping it all straight. Just have 1 entry for 99% of the people and places, but ADD descriptions for each version of earth. Make sure you label them in bold at the top and you'll be able to keep it straight. Plus, your players can review what versions they've seen before in a nice neat format.