Unity alters atlas on build

[ghoulfool]

I've just done an iOS build and suddenly the majority of textures have been messed around with. To explain:, it's like the atlas has been modified and all the references to the textures/sprites have not been updated, so the whole project looks a mess. I suspect that this may have been caused by using too large textures (2048 x 2048?) ,causing Unity to shrink or modify the textures/atlases in the scene

Firstly, Is this an NGUI or Unity thing (or a combination of both)?
Secondly is there a way to prevent it happening again? - Use smaller textures!
Thirdly, I've got a back up of the project but is there a quick and simple "undo" if this were to happen again?

Thanks

[ArenMook]

Check your quality settings. By default mobile platform builds target "Fastest" which reduces texture quality and disables shaders. Make sure your platform build is set to support 2k by 2k textures.