Removing a seat is a terminal action. It cannot be undone once it has been submitted.
In Atlas, navigate to the Customers tab
Search for and select the desired customer to open the Customer page
Scroll down to the Features & Services section, then select the Seat Packages tab
Check the box in front of the seat or seats you wish to remove
Press the Remove button at the bottom of the section
Select if you want to retain the number, if you are porting the number out, or if you just want it to go into aging status as normal
Confirm your selection
The seats will now be locked and unable to have further changes ordered for them (you will see a red lock icon). After a few minutes (usually 5 or so) the seats will be removed entirely.