Is there a way to keep overwrapped UV Islands during texture atlasing?

I have a bunch of 3d models with 4 materials, and every model has duplicated/overwrapped UV islands. Used same texture for multiple building floors and walls, windows and doors, even some buildings just the same texture with completely different shapes.

But after the texture atlas, all UV islands were separated into independent areas, regardless it has duplicated UV coordinates or not.

This makes the overall texture quality terrible, every texture is super blurry, even just combined 4 materials to 3 materials.

Is there a way to keep those duplicated UV coordinates while in the texture atlas progress?

I think you have to be more precise about what you want.

What does this mean ? If you are makeing a texture atlas (maybe plugin) then you are changing the UV’s…
and if you keep you UV’s then why making a texture atlas ??