We currently cannot do this because the material import option are not save in the asset import data, so it search only in the local folder of the reimport mesh, those settings should be saved
Create Material MyMat_A under content folder Meshes/Materials
Create Material MyMat_B under content folder Meshes/Materials
Import attach SphereMatA.fbx under content folder Meshes/Spheres/
Reimport SphereMatA with the attach SphereMatB.fbx file
In the material conflict dialog click "Reset To Fbx"
RESULT: The material MyMatB is not assign to the material slot
EXPECTED: The reimport find the Material MyMatB and change the material slot to point on it.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-86399 in the post.