Follow up:

It turns out that the first step, un-setting the flag, took 7 minutes to run and a side effect was that all users connected to any [or so it seems] database on that server lost their connection. 🙁

For anyone else who tries this you may want to run that in scheduled downtime in case the effect I had will always be a side effect. Its just possible that it was the need to stop/start the Broker service and that that needed a lock on SQL Agent, so perhaps manually stopping SQL Agent first might speed up that step.