Error on Automated Build when multiple instances of Unity are open

Hi,

I have a build script that I want to run in the command line.

C:\Users\me>unity.exe -quit -batchmode -nographics -executeMethod CommandB
uild.BuildUniversalApps -projectPath C:\Users\me\Documents\Development\Uni
ty\Projects\2DPlatformer

This works fine when I have the Unity project window closed. But if I have Unity open with the project loaded, I can't make a build anymore.

C:\Users\me>unity.exe -quit -batchmode -nographics -executeMethod CommandB
uild.BuildUniversalApps -projectPath C:\Users\me\Documents\Development\Uni
ty\Projects\2DPlatformer

C:\Users\me>
Aborting batchmode due to failure:
Fatal error! It looks like another Unity instance is running with this project o
pen.
Multiple Unity instances cannot open the same project.
Project: C:/Users/me/Documents/Development/Unity/Projects/2DPlatformer

How do I fix this issue?
Thank you for your help

Why I want it: I have a Unity project exported to a Windows Phone platform. My workflow is as follows: make scene and asset changes in Unity. Then go to Visual Studio (with the Unity C# project & Windows Phone project opened in the same Visual Studio Solution file), make code & script changes. Then play to test in Emulator... the new build picks up the script changes but doesn't pick up the Asset changes that I made in Unity. I want to add the Unity build commands to Visual Studio's Pre-Build events.