Have you tried to reload the permissions.yml fine within the Bukkit root folder? Unfortunately due to the way Bukkit's written, the only way to do this SO FAR was to /reload the whole server or restart it.
We all know reloading can cause problems, and a ton of them. I made a plugin for the Minecraft Cloud Network that utilizes Reflection to reload permissions for the Server.
This plugin is especially helpful for servers who want to use SQL based permission systems (zPerms) but have different permissions for each server, they can use permissions.yml to create their own custom permission strings for each server. For example:
ServerA has permission essentials.pay ServerB has permission essentials.tpa These permissions must be seperate for each server, make a permission string in permissions.yml of ServerA called my.custom.permission.servera and add essentials.pay as a child node. Do the same for ServerB and add essentials.tpa as a child node. Add a global permission called my.custom.permission.servera/serverb and watch the magic happen :)
Also many thanks to Me4502 for helping me with development of this plugin!
Note: This plugin will not go on Bukkit, why? Cause Bukkit really doesn't know how to respect the community. (Yes I was banned for forgetting to change the text of a placeholder.)
Currently there are no permissions to the main and only command of this plugin, I'm not sure if permissions would even work... So for now you NEED to be OP to be able to run the command, or just do it via console.
/reloadperms - Basically reloads the permissions from permissions.yml
I don't currently have anything in mind for the future of this plugin, however I'll try to keep it updated with the ever changing Bukkit source.
If you like what I'm doing please donate here.