I chatted with a rather unhelpful agent about this wanted to see if I should have hung up and tried again.

Booked X-Y-Z by company in coach. Upgrade cleaned Y-Z but not X-Y. The night before my flight I realized I could buy the one remaining seat on X-Y for what I deemed a reasonable price. I was 2 on the upgrade list so this seemed like a good risk to me. The agent told me I'd lose the Y-Z ticket and there was nothing she could do to protect it.

Is this accurate or is there a way I could have bought this without buying another Y-Z? I know I should have just bought the app upgrade offer a week ago but it looked like there were a ton of seats open. Any cancellation refund goes to the company so I was trying to buy as little as possible with my money.