Again, sorry to re-open this, just wanted to add some united website material.
I'm running into this now again (at 2 months prior, the international upgrades went to waitlist, even though only 5/40 seats are taken), It looks like Acornragazzo and Kacee are correct:
What is the refund policy for MileagePlus Upgrade Awards that do not clear the waitlist?
If you request an upgrade using a MileagePlus Upgrade Award, and none of your travel segments are upgraded, then we will automatically redeposit your miles and co-pay. In most instances, a MileagePlus Upgrade Award will be considered used if any segment of your travel is upgraded. However, if your travel includes requested upgrades to United BusinessFirst® and/or United Global FirstSM, and none of the United BusinessFirst or United Global First segments are upgraded, then your MileagePlus Upgrade Award will not be considered used, even if you are upgraded to United First® or United Business® on another segment. In these instances, we will fully redeposit your miles and co-pay. When applicable, these refunds will occur automatically seven to 10 days after travel.
ref:
http://www.united.com/web/en-us/cont...rade-faqs.aspx
With this info, I think I will upgrade each way separately, so they hopefully clear/don't clear independently. I would hate to drop double the miles/$ and then only get one of the international legs to clear.