Is this a rented server, or on a machine you can access?
if you can get to the game.db you can still back it up, no one can be on the server during this process.
if you are using the excellent Conan Exiles Dedicated Server Launcher it has tools to back up the db using the relocation method.
once the db has been backed up, either by relocating it or archiving,
you then can start over by deleting the game.db and then restart the server which will create a new one,
then log in change the server settings, create a new character. exit stop the server. restore the original game db and restart the server, everyone will be right where they left off. and the settings will stick.