Good news for you. I believe that mileage upgrades have TOP priority for standby upgrades. CO will hold from EUA a few seats for revenue on the SFO-EWR portion, so no matter who is flying, you should be able to snag one of those if you check in super-early. Just make sure that when you get the upgrade issued, they acknowledge that you are entitled to an upgrade on the domestic portion, too, when it becomes available. And when you check in, make sure you're on the standby list for the upgrade.

My brother flew ZRH-EWR-SFO last July and we did this exact same thing. In the end, he got the EWR-SFO upgrade.

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Elite since the year I started making my own travel plans.
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