Solution
LabVIEW NXG enforces file hierarchy. As a result when you right click the project and add a file that is not in the same folder as the project, it will add a 'Link' in the project to the location of the subVI you have added.
If you want to add the VIs themselves to the project, you will need to include them in the project folder on your computer. For example, if you add a folder called SubVI to the project's folder it will look like this:
Now the LabVIEW NXG project explorer will shows these changes:
NOTE: You will need to right click the SubVI folder and choose to
Include.