The only solid reference I can find to this usage of the phrase 'Broken Arrow' is from Hal Moore and Joseph Galloway's account of the Battle of Ia Drang, We Were Soldiers Once... and Young. This is the specific section:

Beside me in the battalion command post, the Air Force forward air controller, Lieutenant Charlie W. Hastings, twenty-six, from La Mesa, New Mexico, radioed a special code word, "Broken Arrow," meaning "American unit in danger of being overrun," and within a short period of time every available fighter-bomber in South Vietnam was stacked overhead at thousand-foot intervals from seven thousand feet to thirty-five thousand feet, waiting its turn to deliver bombs and napalm to the battlefield.

The scarcity of any other references to 'Broken Arrow' being used in this context could suggest it was either unique to Ia Drang, or to Vietnam more broadly. It's possible, for example, that it was just the agreed code phrase for that day or week, or for that specific operation. As I say, I can't find any solid sources for its use beyond Vietnam — only anecdotal/colloquial accounts.

Overwhelmingly, 'Broken Arrow' is used to refer to an accident involving nuclear weapons that does not create the risk of war. The US military's nomenclature for reporting nuclear weapons incidents is standardised by the Department of Defense/Joint Chiefs of Staff. The Native American-themed code phrases (Broken Arrow, Empty Quiver, Bent Spear, etc.) date back to the 1960s, according to Eric Schlosser's book on US nuclear weapons safeguards, Command and Control. The phrase is used in that context in this 1967 work on nuclear weapons safety, for example.

It's very unlikely that the phrase has been widely or commonly used in another context, if it risked creating confusion — particularly if that confusion related to nuclear weapons security, where the potential consequences could be dire.