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@Gordon
Long-pressing the button should be the best way to stop what's running in RAM. Perhaps try doing that before you disconnect
I think the issue could be that when running code normally, the Bangle will run some code that enables ANCS (the bluetooth function that allows it to get notifications from iOS). When experimenting running the flashing LED in RAM it's possible that doesn't get called, so ANCS isn't set up.
So then if the iPhone ends up connecting when it's not enabled, it doesn't see your Bangle providing ANCS when it connects, even if it is enabled at a later date when you long-press the button to reload the clock?