Hi David,
This issue is something I've been a bit worried with myself as we have been dealing with clients with the Greener Homes program who have already "ordered windows" and are hoping that they comply. Some window supply companies we've been working with are absolutely not helpful in cross referencing their own products against the NRCan listed eligible windows as their product line names on the quotes often are not the exact same name as listed on the website. When requesting that they due their own due diligence on their end for their own clients, there is a ton of pushback. As an EA, it's not necessarily our responsibility entirely and there needs to be cooperation between the two industries for our mutual clients. Luckily, at this point, we haven't run into your issue.
In this situation, I would contact the supplier directly with the quote and photo evidence of the windows installed and let them know that there are discrepancies and that the windows quoted qualified for rebate, while the ones installed did not. Ensure it is in writing as well. It will be up to them to rectify this situation on their end and fortunately, you have done all that you can do as an EA. I would also connect with Enbridge to let them know of this issue in advance. They will provide guidance for conflict resolution pertaining to their program.
This is a good example of why it's important to review quotes from suppliers in advance and I think you did your due diligence to prevent this from occurring, but this situation is the window suppliers responsibility to resolve. Good luck and please keep us posted.