If a rate is linked to both the Booking Engine and External portals, then you cannot activate the Stop Sale or set the availability to 0, as this would mean closing it on all the platforms.
You should then hide the rate from the Booking Engine, if you only want to do it there.
Access the Rooms/Apartment section > click Edit against the rate of your interest, the set this entry to No and Save at the bottom of the page:
Hope this helps
Kind regards!