Using texture atlases effectively on mobile

Hi,

I am currently working on a 3d mobile game and intend to use texture atlases where possible. What I am struggling to work out though is how to support Ultra, High and Mid texture assets without having to remap my UV's every time an atlas updates.

Lets say I have 80% of my final textures for one of my scenes in an atlas and I texture my meshes in Max and export them into Unity. Later I then add some more textures into the atlas and this moves the textures around to get the best fit, I then need to shift the UV's on my meshes and export them again. Maybe I could find a way to not move the existing textures already in the atlas but this won't give me the best use space.

If that is the only sensible approach then it still leaves me with the issue of the lower resolution assets. Say I want my High assets to be 75% of the size, they will be packed in a different order to the Ultra atlas, meaning I will need a copy of all my meshes with different UV's. This quickly becomes hard to keep on top of.
The only way I can see to solve this is to take my Ultra atlas and reduce it by 50% in Photoshop to 1024 x 1024 and then the Mid to 512 x 512. This will mean everything is in the same order but I have a feeling that a 512 px atlas is going to have some very blurry assets.

Is there something I am missing? Am I approaching this in the wrong way? Any tips and advice would be appreciated.

Thanks