Hi,
In the Deployed Files tab of the "Deploy Teststand System" tool you will find a button called "LabVIEW Options". From there you can lock your block diagrams (with a password). Locking a diagram is less severe than completely remove it, but the purpose is the same: protect your code.
If you still want to remove the diagrams, you can remove them within LabVIEW (Save with options).
regards,
Alejandro del Castillo
Application Engineer (ni)