I believe this would require much more time/effort than the benefits justify. It would probably also make FlashFXP slower, and would introduce many bugs.
However, I agree that having 5-10 instances of FlashFXP in the system tray is a bit annoying. So, how about having FlashFXP add a single icon to the system tray which expands into a popup menu, displaying all active FlashFXP sessions? This way you only have one icon, but can easily access any session.
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