The new behavior is intended. 4.16 allows users to modify section material slot and not lose any data when re-importing.
In Main the cube Section0 LOD material is replaced with the DefaultGrid material which is also not expected.
This appears to be a regression from 4.15 based on the test execution history.
Result: Cube in the viewport remains a Lime color
Expected: Cube in the viewport reverts to Cyan
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-42739 in the post.