I needed to disable all the alerts on the SCOM server which required me to disable all subscriptions.
From the Operations Manager 2007 R2 Powershell I was able to run the following command
Get-NotificationSubscription | Disable-NotificationSubscription
After I was complete I ran
Get-NotificationSubscription | Enable-NotificationSubscription
which turned all alerts backs on. BE WARNED, it will send all alerts that are in the queue.
There is a tool which will allow you to stop and start all notifications without sending alerts that are queued. It is located at