How to reproduce
1. Download user's attached project "PhoenixPointStripdown-ScriptableObjectsBroken.zip"
2. After opening the project in the Assets folder right-click on the "Code" folder and select Reimport.

Expected result: Script does find the reference to the necessary namespace and none warning are thrown
Actual result: Console throws a bunch of warnings "No script asset for Asset. Check that the definition is in a file of the same name." will pop up.

Reproducible with: 2018.2.3f1, 2018.2.4f1, 2018.4.5f1
Not reproducible with: 2018.19f2, 2018.2.2f1

Note: Take a look at a warning "No script asset for RemoveActorEffectDef". Check that the definition is in a file of the same name." Selecting the mentioned scripts should show in the Inspector window at the top: "No MonoBehaviour scripts in the file or their name does not match the file name". Even though the filename does match the class name inside.