First question is.. which is better... absolute or incremental encoders?
Either an incremental or absolute encoder will create the windows, but how do you want to track the actual window position? Personally I would use an incremental encoder. You can actually use an incremental encoder to both create the window AND accuractly track the window position.
Lets say each window is 20 counts long and Check in Counter 5 is at the encoder count position 250, but you might want to signal Check In 5 to drop the bag when the window reaches 230, or 240 etc.. So in short the incremental encoder will allow more flexability in the final setup.
Regarding assigning windows. You maybe should assign windows to the counters on a 1st come 1st served basis. OR you might find it necessary to priortize them by which bag has to get to what gate in time for it to make it's flight. If the bag at check in 5 has to go to a flight in 5 minutes, but the bag in check in 1 leaves in one hour, you would want the bag in 5 on the conveyer before the one check in 1.