By default No. It scans for player structures in a radius and if found does not upgrade that area. You can make it very mercenary and upgrade everything which may damage o remove builds but not by default: The Mod Author JereKuusela thought of that :)
Upgrade_World by JereKuusela
Download your Servers database locally and try it to avoid any possibility of smashing your hard work. If it then works re upload the adjusted db. Thats what I did.