When you refer to a file script in a watch, the watch itself is not updated if you change the script on the filesystem.
Currently, the only way to reload a file script in a watch is to delete the watch and recreate it.
When you create a new watch or edit an existing watch, if you navigate away from the page without saving your changes they will be lost without warning. Make sure to save your changes before leaving the page.
When X-Pack security is enabled, a watch stores information about what the user who stored the watch is allowed to execute at that time. This means, if those permissions change over time, the watch will still be able to execute with the permissions that existed when the watch was created.