I've got a few respondents who made it 95% of the way through a questionnaire, but for whatever reason, didn't complete it. The response is marked as "Complete = No". Another external process uses this field to determine if additional action should be taken. If I mark the response as "Complete = Yes", will this trigger the confirmation email to be sent (I don't want an email to be sent as some of the responses were started some time ago). Thanks in advance.

I don't think that will send the mail, I think sending is triggered by the form submission.

...but it should be easy to test.