Make sure you keep the parents connected with Full Control and remove all other adult connections that are no longer needed before you make this change.
After doing this he will disappear from the unit roster however you can still see him by going into your My Profile > My Connections page. If he joins Scouting again just edit his profile and select the unit again.
Alternatively, if the Scout is still part of your unit but is inactive you can do the following:
Just go into your roster and edit their profile. There is a button option to disapprove them.
This takes them out of your subscription but maintains a connection with them so you can easily pull their records. If you need to add them back, just edit their profile and check the box that you approve them.
Some units create a special den or patrol just for inactive Scouts. If you don't want the inactive den/patrol to show up in reports just disapprove it as well.
How do I transfer a Scout to a new unit?