Thanks Sisso, I had a look over your project and the links, I'm already doing all the things that people are recommending but some of my atlases still aren't setting.
Hi Aren, All my widgets are set to reference atlases. When the project starts I'm getting the path to all my reference atlases and switching in either the 'HD' or 'SD' path. All reference atlases and replacement atlas paths are being found at start up, although only a few of my reference atlases seem to be setting the new path. The items in my first scene all seem to set correctly, but by the time I'm getting in to my second scene I'm noticing that some of the reference atlases aren't set correctly.
When we quit playing the project in Unity, we can see this behaviour clearly on the reference atlasses: not all of them have updated to the correct replacement atlas.