Is there any way to merge two worlds? Like take chunks from World A, and put them somewhere in World B?
With external programs like MCEdit you can copy parts of your world to files and then import them into the other world.
The question sounds like you want to overwrite all chunks of world B with all chunks from world A, but nothing else.
In that case you just have to delete the folders "region", "DIM1" and "DIM-1" from the world folder of world B and copy those folders from the world save folder of world A.
But careful, this can have a lot of unexpected side effects. For example you would keep your ender chest from world B, even though it looks like an external inventory like a chest.