To clarify my current predicament - I am able to upgrade with Avios for fares booked through corporate travel agent, I have a 125- ticket number etc

The frustrating part is it takes 45+ minutes of both my time, and the time of a BA agent; who arguably could be doing better things and I do feel some level of guilt taking up time to do something like this, when they could be helping a customer with a potentially more serious issue.

We do have the option of booking directly ourselves, and claiming back through expenses (which makes upgrades significantly easier) but comes with additional risk if we need to cancel or reschedule the flights