I selected auto upgrade for a flight from JNB to LIS from Y to J. I got auto upgraded on the DXB to LIS sector a few days before flight. I then received an email suggesting I pay to upgrade JNB to DXB sector. I did not have enough miles to upgrade each sector individually (nor would I want to) but had had enough to upgrade both legs in one go.

I called EK in US and the agent cancelled the auto upgrade and reimbursed me my miles. She then upgraded me on both sectors at the reduced rate when upgrading both sectors simultaneously.