Update: I sent an appeal email to ottpilot-immigration@cic.gc.ca 25 days ago, and didn't get any reply. I sent again 15 days ago, still no reply. I also sent an email to "Case Review Immigration" as I have seen a presentation from 2011 saying:
Please contact us if:
• You have a case where there are exceptional circumstances
(example: urgent protection cases)
• There is a case that may not have been appropriately dealt with by
a CIC local office or visa office and where litigation is to be avoided
• If you notice a number of cases in which you believe there exists a
pattern of concern.
• If you have not received a reply to your enquiries within 30 days of
contacting a particular visa office.
E‐mail: Case‐Review‐im‐enquiry@cic.gc.ca
They didn't reply either. I'm giving up

I put together a new application for PhD stream, wrote a more detailed employment letter following the tips and successful letter templates in this forum, and sent out today. Wish me luck...