Great question — answering as the UphillTech team:
Answering my own question. I did reach out to the embassy visa web form and explained the situation. They had requested to submit my passport again and my application was processed. I am in Canada and want to thank everyone who wanted to help. Hope this helps others.
Full answer by Divakar Manivel: https://travel.stackexchange.com/a/202829 (CC BY-SA 4.0).
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