Your other options is to turn off All board subscriptions which is a setting under Admin/System/Subscriptions. The hover text next to this setting says this: Disables the option for users to subscribe to boards. Existing subscriptions are also turned off, and email notifications associated with those subscriptions will no longer be sent out. So you could turn if off while you do the update, let people know subscriptions are down for that period of time and then turn it back on when complete. I am unsure though if any notifications accumulated during that down time will then be sent out once you turn this back on.
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