Lee, what's the condition of the window frames? Is the water coming down from where the two frames over lap? Or Is it a problem with the finish, putty paint etc.
Re- reading your post I see what your on about. As has already been said, regarding ming in that gap then a good scrub is the only option with the water off I think, unless you can get up there to clean it out trad, or gutter vac it
Thing is, I'd say depending on the condition of the frames you'd want to be careful not to damage the seal and paint if it's already in a poor state.
You're always going to get water held in there for a while, I wondered if poor putty and paint around the top of the top frame might also cause the same problems. UPVC and ALI being so smooth in comparison.