Steps to reproduce:
1. Open the attached project(CompilationError.zip)
2. Build for Windows Standalone (x64) -> There build should fail because of a compilation error in NewBehaviourScript.cs.
3. Open NewBehaviourScript.cs and remove the "using UnityEditor;", return to the Editor
4. You will get the following error:
Assets/Code/Imagine/Editor-Tools/Build.cs(3,7): error CS0246: The type or namespace name `FunHouse' could not be found. Are you missing an assembly reference?`.

Expected result: Unity should not throw the error
Actual result: After a build fails and a compilation error is fixed, the assemblies are not being updated (Unity keeps using the runtime Assembly-CSharp-firstpass.dll) and Editor scripts in the Plugins folder are not included in the assemblies

Workaround:
Reimport the assets or restart the Editor

Note:
Unable to test with 5.4/5.5 due the errors

Reproduced with: 5.6.1p1, 5.6.2f1, 2017.1.0b10, 2017.2.0a4

Fixed in: 2017.2.0b2
Backported to: 5.6.3p4, 2017.1.1p1