Is there a way to change all devices using protocol X to protocol Y.
I'm changing the name of a Plugin and all connected devices need to be moved from the old to the new name.

The plugin protocol name is cached by the Indigo Server and there is not currently a method to clear that cache. However, if you open the device dialog, change the device to a different plugin, change it back, then OK out of the dialog it will be recalculated (I think).

Note the protocol name being old or stale isn't a huge issue since that name is just used in the UI and not used internally to look up the owner of the plugin. Maybe a bit confusing for users, but only for those already using the plugin and early adopters are normally pretty understanding.