Entries in a jar/war are not files. You should refer to properties (and any other kind of resource in a war) using clojure.java.io/resource
instead of clojure.java.io/file
or a bare path string. This will work for local resources on the file system as well as resources in a war.
You can put the resources in the resources dir in your project root, or in other dirs specified by :resource-paths, then they are available on the classpath and also will be included in the war when you build one using lein ring.