They don’t roll on their own. Charges recharge consecutively, not concurrently. So long as you don’t overcap charges, and you end the fight with zero charges, you have never lost a cast of Aimed Shot, and thus have not lost any DPS.
If you chain cast both charges, you need to wait 9 seconds for the first charge, followed by 12 seconds for the second. That’s consecutive.
If they were independent concurrent charges, you could chain cast and have both charges back in 15 seconds. That isn’t how it works.