Sending a webform enquiry to submit passports at Indian VFS is not a tough option. Lots of people do that.That's what I thought; my parents are in India so request to submit passports at Vfs in india or NVDO would be the logical option.
That said, I do travel to India at least once every two months, so if timing works, I could being their passports...
I have no previous experience of hearing anybody bringing passports to Canada to get stamped. Most probably should not be anything wrong with it, unless customs stop you for checking your bags for some reason and find 2 extra passports in your bag (truly belonging to your parents and their COPR letter has good reasons), may be they hold you for security check for long.
So go with changing the Visa office, it will ALLLL work out perfect