If you tick that then when you reimport an FBX we will try to preserve any custom materials you set to the various mesh instances. It’s not perfect - if you remove mesh instances from your model there will be some wrong assignments and you will need to fix it but should be OK for now.
I did have a mess up were a model was missing from the FBX and that messed up like you guys said it would,
but putting the full model back fixed it no problem easy peasy, but today the model reverted when re-importing around 4 PM EST. Full model (using a selection set to ensure nothing goes missing) and it reverted back to light maps and those were messed up on some models.