How to change mesh UV's permanent in Unity (texture atlas)

I have made a texture atlas generator and the only problem is that it is not permanent. I generate the atlas, change the uvs on the different meshes and then assign a new material with the new texture. It all looks perfect until Unity reimports the meshes. Is there a way around this? Maybe stop the reimport process for certain assets or save a copy with the changed UVs? Or is the only fix to do it in the fbx’s themselves?

i try not to directly use fbx files. you just need to change your workflow a bit.

or you can export your models into outside unity folders than manually copy them in, u still going to have overwrite issues if its the same name.

one thing you should always do is once fpx is imported is to make a prefab out of it. if u still having issues, then u can also change the mesh’s attached to the object to a custom mesh you do this by selecting the mesh in the mesh render.

so import fbx make a new prefab out of it, and change mesh data to your custom one