Just do this. Hundreds of material instances can be made instantly and not a single one will need to compile. In fact, you can generate new materials DURING THE GAME with material instances (this is useful for user generated content, where instead of making an actual new material, you just make a new material instance and plug the user’s content into the parameters).
I would say just replace the materials on the meshes with material instances, but if there’s a lot of them, that would be tedious. Plus, there may be things done that are completely unique to just that material.
However, for simple materials, you could make a blueprint to automate this, where it goes through each folder, finds materials, gets the textures in those materials, puts them in material instances, then replaces the materials on the meshes with the instances. I’ve done something similar to this, so it should be possible; read this post to get an idea (you just need to read the material and mesh sections).