I doubt anyone will be able to help me as I have a feeling that the way I'm doing things might not be the most common way, it's just a solution that I found to my problem but I'll go ahead and describe my issue.
I have a scene that has a lot of objects, however many of them are copies. I'm trying to export everything in my scene to Unity so I figured that I first need to create a texture atlas to reduce the draw call by only having 1 material.
What I did was make a copy of each unique object and dragged it aside. Once I had one of each I joined all of these objects that I dragged away from my scene. I created a new UV map, unwrapped everything and then baked all of my textures on a new image. I then deleted all the materials and only kept the new UV, created a new material and used my atlas texture as the texture image. So far so good.
I then grouped up all my duplicates from my scene using ctrl+g so it's easier to select them. I then went to my joined objects and separated each by selection. Then I selected the group of duplicates from my scene and the object that I just separated which was now using the atlas and I linked my materials and uv map with the others that were the same. I did the same for every single object in my scene so that all of them were now using an atlas texture. All the objects in my scene basically copied the UV map and the material from the objects that were dragged aside and joined to create the atlas map.
Once I did all of this, I then took all of the objects from my scene and pasted them into a brand new blender document. I joined them and then I moved forward to import the object into Unity. In blender it only shows me as having 1 UV, 1 Material and 1 texture for all of these joined objects. In unity however the object comes with around 250 separate materials, one for each object that I joined. How can I remove all of these materials and have unity only use my 1 material with the texture atlas?