Import into level replaces the materials you assigned after reimporting the level. I made a level with some placeholder materials, then in UE4 replace them with the material instances created from an environment master material. Next I fix some meshes and do Import into level again, but now all of the materials are reverted to the placeholder materials.
Import into level shouldn’t revert material assignments because it messes up the iterative workflow. Unticking the materials on Import into level reimport doesn’t help, it just removes the materials from some of the meshes (strangely not all of them).