Although this may not be the answer the OP wants to hear, this is how AA does upgrades.

e-500 (domestic "sticker" upgrades) are not transferrable upgrades. The underlying ticket is still considered guaranteeing only a coach seat. The upgrade is truly space-available, and if anything with that space changes, you have to go through the waitlist again. It's a good idea in situations like the OP to monitor flights carefully in case of bad weather, etc. To hold a desirable upgrade in R class, proactive discussion with AA may allow you to prevent an automatic rebooking.

However, SWUs and BXPs do "stick" with changes to the reservation. They also book into C class domestically while e-500s book into R class.