It will not over-ride any workouts they have programmed on their own. It will over-ride any existing workouts that you have published previously on that date. If you re-publish a certain date, we assume you want the customer's day to look like your day. i.e. Any workouts subtractions/additions will be done.
Note this sort of weird potential situation:
1) Publish Marketplace workouts to a customer:
Wednesday: Workout "A"
Thursday: Workout "B"
2) The customer decides to swap workout "A" and "B", customer's calendar now looks like:
3) You (Marketplace publisher) finds a mistake in workout "B", makes a change to it, and re-publishes "B" to Thursday. SugarWOD "clears" the customer's Thursday of all publisher workouts and re-publishes "B" to Thursday. Calendar now looks like: