how does the mesh filter chose which material to use in a multiple material 3d model?

The Problem

I am working on a tile-based project and I need to switch the mesh filter of tile at runtime. On this tile object, I have two materials, one top material, and base material. But when I change the mesh filter of a tile(to have a different look to the tile), it swaps the two materials of the 3d model. Some types of tiles that I swap are fine and have the correct material assigned to the specific faces, but most of the materials are inverted.

Things that I tried

So I tried to see if this has to do with the order of the materials in my 3d software blender, but the order did not do anything to fix the problem. I tried to invert the two materials in blender, but this also did nothing. Only if I assign a different face to a material I will see a difference in the model. And if I try to do this face by face to make the material not inverted, it will eventually switch back to the incorrect material placement. Overall, I just keep getting inconsistent errors and I don't know what to do to debug this. My guess is that unity makes the order differs depending on the number of faces that a particular material has(and that has to do with the mesh filter). Or I am using blender incorrectly and have some sort of bug with the model. here's some screenshot to better visualize my problem : ![alt text][1] ![alt text][2]

conclusion

If anyone has any insight on how I can fix this problem it would be most appreciated. I would like to know more about mesh filters if possible, the unity documentation doesn't provide the information that I need to solve this. it would be nice to know how does the mesh filter chose the material if they are multiple ones for example.
[1]: /storage/temp/187133-screenshot-8.png [2]: /storage/temp/187135-screenshot-4.png