Joie, great to hear from you (if this is the Joie I know so well!).
When you apply a plan, it won’t remove or over-write anything already on the calendar. It WILL double-up the workouts. For example, if you have Plan A that starts on March 1 and Plan B that starts on May 1, but Plan A is 12 weeks long, then for all of April you will have both plans on your calendar each day, and TP does not make it easy to identify which plan belongs to which workout.
So, the best thing to do is to load Plan A and Plan B, and then just remove Plan A from your calendar when you are ready to start Plan B. Removing a plan does not remove any past completed workout, removing a plan only removes past incomplete workouts and future workouts.