Solution
LabVIEW creates an application instance for each target in a
LabVIEW project. When you open a VI from the
Project Explorer window, the VI opens in the application instance for the target. LabVIEW also creates a main application instance, which contains open VIs that are not part of a project and VIs that you did not open from a project.
To specify the application instance, you need to get the reference of the target you want to use and use that reference to run the VI as show in the figure below.