Steps to reproduce:
1. Open the attached project (MinReproUnityProject.zip)
2. Open the Assets/scene.unity scene
3. Switch platform to Windows Store
4. Build for WSA Universal 10 (.NET backend), Build type - D3D, Enable C# projects
5. Open Visual Studio solution
6. Deploy on local machine (DEBUG/x86)
7. Go into the Output folder and make these files(project.lock.json, project.json and Package.appxmanifest) read-only
8. Build the solution again (with all the same settings as step 4)
9. Open Visual Studio solution
10. Deploy on local machine (DEBUG/x86)
11. Deployment will fail

Expected result: Deployment should not fail
Actual result: Deployment fails

Note:
With 2017.1.0a2 it throws UnauthorizedAccessException (Step 8)
With 5.5.2p2 it throws UnauthorizedAccessException (Step 8)
With 5.4.5f1 it throws UnauthorizedAccessException (Step 8)

Reproduced with: 5.4.5f1, 5.5.2p2, 5.6.0b11, 2017.1.0a2

Fixed in: 2017.1.0b4
Backported to: 5.6.1p1