I eventually called again this morning as advised by the AA rep yesterday, and that other person told me they wouldn't re-ticket after a Business Extra upgrade. Checked my inbox just in case and nothing came in today neither. Not really sure what to do here, don't quite like when multiple reps contradict each other, but was also told I had nothing more to do on my end so...

To your point I actually found pretty disturbing that the baggage allowance was not clearly displayed next to each flight in the confirmation email, or at least in the upper part somewhere. It is only after having dug a bit in the bottom of the email that I eventually found, in a light gray colored fare rules like paragraph, that the allowance was one bag (that was before the upgrade)
Was kind of surprised that they would bury that info so deep in the conditions. I actually even had to click 'display more' on Gmail to get to that point of the email. I guess it's probably not violating anything since it is here somewhere, but I wouldn't be surprised to hear that some unfamiliar people got mixed-up because of that. I have the overhaul feeling that AA's information system has been getting pretty old lately.