Steps to reproduce:
1. Create a new Unity project
2. Create a new Scene
3. Build for UWP to an empty folder (make sure scripting backend is selected to .NET)
4. Open VS solution
5. Build & deploy on local machine (Release x86)
6. Exit player and Visual Studio
7. Go to the player's folder
8. Delete "UnityOverwrite.txt"
9. Repeat steps 3 - 5 (overwrite the previous build instead of building to an empty folder)

Actual result: build fails with an exception thrown

System.Exception: AssemblyConverter running on already processed assemblies. There is something wrong with your build.
at Unity.SanityCheckStep.Execute()
at Unity.Step.Execute(OperationContext operationContext, IStepContext previousStepContext)
at Unity.Operation.Execute()
at Unity.Program.Main(String[] args)

Reproducible with: 5.6.3f1, 2017.1.0p3, 2017.2.0b6, 2017.3.0a3

Not reproducible with Debug configuration

Fixed in: 2017.3.0b8, 2018.1.0a2