So sometimes... I'm not the sneakiest assassin. I've encountered various occasions where I've spooked a Borgia Captain that knew his number was up. He runs off, and I'm notified that he'll return when the guard shift changes. At that point I either give up or busy myself killing his guards till he shows back up. Ideally though I'd like to know how long to wait, and just go do other things nearby till he's back. Is it a fixed period of time, and if so - how long?
You have to wait till it's Dawn/Dusk.
The Guard shifts change at dawn and dusk in the game. At this point, the Borgia Captain who ran away comes back.
There is no fixed time in the real world for dawn or dusk to take place as it fluctuates in the game. But you will obviously know when dawn/dusk does happen in the game (as the color of the sky changes) and thus you can complete/abandon what you are doing and go burn that tower!