i'm guessing it has to be a different timeline? or maybe there was an uprising and nook and isabelle are fleeing to a deserted island for reasons lol, if it were to make sense chronologically
I feel like its a different dimension/timeline. Kind of like in the tv show LOST where they "create" different timelines with each other in them because they are all connected <3
I like to think they abandoned the NL town, but there are plenty of NPCs left there to keep things running.
The player character of NH is not the mayor of NL, or you'd think Tom Nook or Isabelle would acknowledge them or make references.
In the Animal Crossing universe, clearly, there is an endless supply of clones of Tom Nook, Timmy & Tommy, Isabelle, etc. because every single town and island has one of each. So, all of the New Leaf towns and all of the New Horizons islands can exist simultaneously, in the same timeline, and nothing is abandoned. That's the conclusion that I've come to anyway. How else can you explain there being another Isabelle at every single other town you visit when Isabelle already lives in your own town?
I don't repeat villagers, as I'd rather be able to experience more villagers than just keep reusing the same ones. I'm moving a villager who has lived in my main New Leaf town out of that town and sending her to my New Horizons island so as not to have a duplicate and so it "makes sense."
Regardless, I see New Horizons as being a sort of parallel timeline to New Leaf, in the same sort of situation as you find in the Pokémon video games with stuff like Omega Ruby & Alpha Sapphire compared to the original Ruby/Sapphire/Emerald. I mean, we have the same shop owners and the Able Sisters have the same conversations as they do in New Leaf, so there isn't really any direct continuity taking place.