Some template designers use Chiefs in their templates, which translate to "Missions In Progress" once the template is initialized. The DCS has a button called "Remove In Progress" which can be used to scrub all these mission plans, leaving all units at their respective starting locations. This is exactly what you want.
This is the same as removing the contents of the Waypoints table, but a lot easier to do (one click and a password).
No need Starfire. The DCS has a trillion buttons now - it is easier than ever for the eyes to glaze over. There will be a few more buttons in new release...