Let say I wanted to fix some visual bugs in an existing route, like floating buildings and so, will this carry over to already excisting scenarios, or would I have to edit each and every scenario to ?
If you change something in the World Editor it affect every Scenario Changes made in a Scenario by going in to the World Editor only affect that Scenario
Don't forget to back up the modified files you produce. A file verify or re-install of a route will remove your mods so you need to have backups to restore from.