(corrected title) Equipment change after check in = UDU request gone?

The second time this happened to me in the last few months. Checked in 20+ hr before the flight and made sure the upgrade request was there -everything looked fine. Showed up at the airport - my name was not on the upgrade waitlist. GA confirmed that once equipment change happened old requests drop off and cheerfully noted that even if he put me back on I had no chance of clearing.
Asked to speak with service director who said it was the software thing but agreed to forward my comments to customer service.

I am not even sure how to handle smth like this in the future - if you don't check in early enough you decrease your chances under normal circumstances but if you do and they make a change you are dropped of the list.

BTW this was LAX-IAD 777 (intl) to 767 (domestic) swap.