Do not send emails when status is changed from one 'counted' status to another 'counted' status (e.g. Do NOT send email for change from Registered to Attended).
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I verified that we are currently 'automatically' notifying participant for this status change AND updating contribution status. Although this is probably reasonable behavior for some scenarios - it can cause confusion if statuses are being updated after the event has occurred.
Work-around is to update participant statuses individually (Edit Participant) - since user can control both behaviors in the full edit form. You can also turn off 'Send Email Confirmation' for the event - altho this will not prevent contribution status from being update.
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I was mass updating the registration status of people who came to our event based on our paper sign-in sheet. I know it was happening to people whose previous status was "Pending from Pay Later," but I don't know if it happened to people who were "Registered" (already paid online).
The effect of this is that a whole bunch of people got confirmation emails long after the event, when I was updating their attendance.
I'm hoping I can fix this by turning off the confirmation email in the event, then marking the rest of the attended people as attended, but I haven't tried it yet.