I am getting an “External Changes” dialogue prompt: what does this mean?
This means that some file(s) managed by Vortex, such as files from a mod you installed through Vortex, were changed by another application. This causes the actual game directory (where the changes have been made) and what Vortex “sees” in the Vortex “mod directories” to be out of synch.
With external tools such as FNIS, or XEdit making changes to files this is expected behaviour and not an error. Via the "External Changes" dialogue, Vortex gives you the option to revert any such changes that have been made to files, or keep them.
Once a file has been changed in one form or another (moved/deleted/edited) by an external application, Vortex will trigger the “External Changes” dialogue the next time mods are deployed or enabled/disabled. You will then be able to either reverse these changes, or apply them. Either will lead to the Vortex mod directories and the game directory to synchronise again.
Bear in mind that once you apply or reverse changes and confirm your choice, there is no way to undo either action.