First off, take a close look to see if it's an adpater that screws on over a schrader. In which case you can remove it without letting anything out.
Can you post a pic? My 05 had schrader valves on both low and high ports, what year is your vehicle?
I agree, the schrader valves are easier to work with, you can use a port tool to remove the valve core to make charging and vacuum far far faster. Pulling a vacuum or trying to fill a system through a valve is unnecessarily slow.
It's a pain to have to suck what's left out just to change a valve but if you have to replace the valve I'd go back to a schrader.