It's been awhile since I've seen WYLB, so maybe it was explained/discussed (or maybe it wasn't) but what exactly happened to the Female Founder after signing the surrender treaty? I thought that, for some reason, she was allowed to return to the GL but I think that I saw something else that stated that she was imprisoned for her war crimes?
Also, what happened to the remaining Dominion troops, soldiers, ships, etc? Did they return to the GQ and if so, how? Did "The Sisko" make some kind of arrangements with the Prophets to allow them safe passage back home or did he- as a Prophet- facilitate their return? Seems to me, with a fleet of Dominion ships waiting on the other end of the Wormhole to come into the AQ, it would've been quite a risk to permit the passage to open. What if the Dominion pretended to surrender, the Federation/Prophets allowed the wormhole to re-open the passage, and the GQ Dominion ships scream into the AQ destroying DS9, Bajor in retaliation for the war and/or finishing off the Federation Alliance?