Reproduction steps:

1. Create a New Project
2. "Build And Run"
3. Add/Remove scene from the Build Settings
4. "Build And Run"

Expected Result: The project builds with the updated scene list
Actual Result: The Build fails with an error

Reproduced with: 2018.3.0a1, 2018.2.0b8, 2018.2.0a1, 2018.1.5f1, 2018.1.0f1, 2018.1.0b13, 2018.1.0b6, 2018.1.0a7, 2018.1.0a6
Did not reproduce on: 2018.1.0a5, 2018.1.0a3, 2018.1.0a1

Note:
Re-Build in the same directory

Sometimes you have to restart the Editor for the bug to reproduce

"IOException: Failed to Copy File / Directory from 'Temp/StagingArea\UnityCrashHandler64.exe' to 'C:/Users/.../Downloads/New Unity Project/New folder\UnityCrashHandler64.exe': destination path already exists."

"IOException: Sharing violation on path Temp\StagingArea\UnityCrashHandler64.exe" or "C:\Users\...\Downloads\New Unity Project\New folder\UnityCrashHandler64.exe"

"UnauthorizedAccessException: Access to the path "Temp\StagingArea\New folder.exe" or "C:\Users\...\Downloads\New Unity Project (2)\New folder\New folder.exe" is denied."