I was able to upgrade one VS segment to PE with miles even though the ticket was booked with Expedia. It may take some going back and forth (took me three agents to secure the upgrade) but if they're willing to put in the effort they can alter a ticket booked with an agency. In my case the third agent put me on hold on and off while she spoke to ticketing. Getting the upgrade approved with the correct fees took the longest time but once it was approved the ticket was modified instantly.