Here's what I did. Using the PP Sandbox, I upgraded a site to the first level. I then upgraded the same site to the next higher level.
When I go to "modify site" for that site I see that both charges went through. When I look at the box, Modify Pro Sites Status, the only cancel, refund etc that is offered is for the first level. It didn't capture the second upgrade.
The subscription information box indicates it did do the second upgrade.
Account History, shows the first level cancelled and the second started (correct behavior). However, each time an upgrade was done, the history shows the following error twice.
"User modifying subscription via PayPal Express: PayPal returned an error: The token is invalid"