I have never seen this happen in any of my playthroughs and I've always saved the Chargers. Where does this happen? War map? If so which quest?
During a War Table Operation chain where you work with the Ben-Hassarath to dismantle the Venatori spy network in Southern Thedas you get word that a Venatori fleet is heading to Denerim and you can call on the Qunari to send a Dreadnought to take the fleet out. If you messed up in previous missions (which will slow down the Dreadnought) or chose a different option for this specific mission (I think the other options are to rally a fleet of Fereldan vessels from the local nobles or just warn the city of an impending attack) Denerim is attacked, half the city is burned to the ground, and there have been conflicting reports but some say that the monarch, King Alistatir or Queen Anora, is killed in the attack.
But like you said, there is no mission to respond to half of Denerim being burned down and the King or Queen possibly being killed from an attack by Teviner nor any word about it in Skyhold or anywhere when you save the Chargers. So either Denerim is attack and you hear no word about it or the attack only happens in response to the Inquisition allying with the Qunari. I'm betting it's the latter since the people who had a Queen Cousland Warden would be beyond pissed if Alistair was killed offscreen because they didn't sacrifice the Chargers.
I really don't think this choice is about Save Denerim vs Save the Chargers. It's more about whether you want to sacrifice the Chargers for Qunari resources and the possibility on this alliance building into something beyond stopping Cory or what is better for Iron Bull, his life as a mercenary or a Qunari.