Is there only one suction line at the pump inlet? I’m just trying to make sure of the plumbing configuration.
That flap, if closed, would stop the skimmer from operating and the pump would pull all the water from whatever is hooked up to that secondary port. So, if the MD were plumbed to the skimmer, then closing that flap would cause the pump to pull water from the MD. In practice, that flap doesn’t make a tight seal so even when it’s closed, some small amount of water will be pulled into the skimmer.