The scroll in mind is called "Settlement Name Change," and you are correct it is a max quantity of one per use. Once purchased, head to the Domain & Settlement Selection portal (the appropriate server selected), and a window prompt will be open for you to rename the settlement. After that it is a matter of time for the name approval to go through, once accepted (if approved) then you will receive a private message here on the website about it. :)
Settlement Name Change: