Concurrent dependant routines in a gui application
Running non-gui related stuffs using the main event-dispatch(gui-thread) is kind of anti-gui practice.
If first process should be called, and then second process, so it's basically a long synchronous calls (with user prompt between each)
Probably(good practice) is run the first long process using a thread(usually out of event-dispatch/gui-thread).
Meanwhile, the long process could inform the GUI about the process by sending progress events(assuming gui works as a process-progress-listener here).
Now, because the long process is run by a thread, gui is functional, and not freezing, so user could see progress, or control the progress(e.g. abort, etc...)
Once the long thread is finished, ask the gui-thread/event-dispatch for user prompt, and if starting the second long process is a thing, go for it just like first one using a thread.
Overall
Try not to perform excessive non-gui stuffs using gui-thread/event-dispatch. This is actually a good practice.
Try not to perform gui related stuffs(such as updating a progress-bar value/status) using non-gui threads(out of widget/dispatch scope). This may not be valid for all widgets, but usually(possible) any gui change(here like progress-bar change) seems to be ignored.
But actually that out-of-scope thread could not force the main-gui thread to perform a refresh/repaint on target component.
Assuming, the-gui/event-dispatch thread is the guy who sitting next to the widget door, and is waiting for any gui-related requests.
So if a request about updating progress-bar is made correctly by the expected routine, that guy will repaint the target progress-bar since it have to.
But what happens when the request came from out of event-dispatch scope? It's more like getting into the room from windows, rather the door, and the guy next to it.
So technically progress bar will be updated, but might not updated immediately(or at all), since the guy who in charge to keeps ui updated did not realized there is a requests that forces component(s) to get repainted.