http://jediknight2.filefront.com/file/Samurai_Village;34493 Does anyone know if this map overwrites anything?
No, it doesn't. The majority of maps do not overwrite anything. If you want to know if a file overwrites anything, read both the file review and the readme, it'll usually say in one or the other.
I don't know how, and I don't know why, but this is totally Sheep's fault.