Reasons why should be preserved or key files moved out for archive:
- The keystore is stored there. No sense in recreating for new server or migrated server with same hostname. http://www.manageengine.com/products/service-desk/help/adminguide/introduction/install-ssl.html
- Customizations to server.xml may be desired to preserve rather than recreate on fresh install. http://www.manageengine.com/products/service-desk/faq-general-modules.html
The in-software mods is nice to preserve, but the mods done directly to the configs should not be ignored.