I booked an Aeroplan ticket a few months ago on my fathers account using his points. He has E35K so I used a priority reward to book the flight. I noticed that until September 2019, it is possible to upgrade on an Aeroplan ticket! I do not have status so I was not expecting that I would be able to do it. Went on the eUpgrade site today, and it is letting me upgrade even though I do not have status! At first, I assumed that it thought my dad was the one travelling, but when checking in I had to pay for two checked bags so I was unfortunately mistaken.

The biz class cabin was full on the first flight so I just checked in without upgrading. Later, I realized that the biz class cabin on my next flight was nearly empty, and I could have upgraded! Wondering if I should try and get AC to refund my baggage fees and upgrade on that flight instead at the airport tomorrow? Or is this likely a glitch in the system? Would be nice to upgrade, but I am not going to risk messing up my flights if the agent thinks something is not right.

Also, an upgrade doesn't entitle you to a refund of baggage fees. With an upgrade, you still have an economy ticket with all of the same features and restrictions, you just happen to be permitted to sit in business class.

His Father has listed him as his nominee (or is that a SE thing only?)

IIRC just SEs can nominate one other person unless you're traveling with the person being upgraded, which is not the case. Also would be copay on AE award tickets.

I am not saying an upgrade entitles me to a baggage fee refund. I would have upgraded on my second flight had I know that I had to wait to check in and complete check-in after upgrading for the second flight. Flying business class means free checked bags, so I assumed under these circumstances a refund is warranted.

My dad's account, I booked an AE ticket on his account. AC has a special on until next September that lets you upgrade from Aeroplan tickets. I was not expecting to be able to use his credits, but for some reason, it is allowing me to do so. Maybe a glitch in the system.

When you went onto the eupgrade site, did you log in with your father's account or your own (even though you don't have status)? Not sure if the latter is even possible.

You're not understanding what I'm saying. Your premise is incorrect. Getting an eUpgrade isn't the same as buying a business class ticket when it comes to things like baggage allowance. See below from the AC eUp site (emphasis mine).

Adam, I don't think there is any need to be rude. All I am saying is, I would have upgraded had I known that it was possible on my second flight. I did not realize this until after check-in. I am logging in on my dad's account and punching in my booking reference. It is listing me as the eUpgrade account owner when I do this. It still lists him as the owner of the credits, but it is allowing me to upgrade for a certain number of points plus an add-on fee.

No one is being rude. I'm trying to provide information and answer your questions in a factual manner.

To wit, based on this thread as well as the second one that you posted, you seem to think that getting an eUpgrade means you don't have to pay baggage fees because you're flying in business class. That's not the case; you still have to pay whatever baggage fees are associated with your original fare - as detailed in my last post.

If I misunderstood what you were saying/asking, then please elaborate and correct me so that I (or someone else) can properly address the question.