Certain import settings with presets cause missing references in prefab and scene :

Reproduction Steps:

2018.2, start new 3D project with extras

In the project view go to ExampleAssets > models > brush
Create a Preset from the brush model using the top right Preset button.
Select the Construction Light model
Apply the previously created Preset using the to right Preset button
Click Apply

Notice construction light disappears in the scene.
Select the transforms and notice linked meshs are either missing or wrong.