This is the main shortcoming I’m working to fix for the Tiled 1.0 milestone. But it’s not trivial and so far it’s leading to a rather big overhaul of the UI.
This should actually work, but it’s tricky. Try overwriting when exporting and then restarting Tiled. As long as your maps are referring to this external file, it should pick up changes saved to it. In any case, I’m really looking forward to getting rid of that hacky workflow.