This has happened to me often at this time of year. The issue will disappear in less than four weeks. Isn't one good thing about e-certs (in theory) that you will only be charged for the upgrades you fly?
Sounds nice in theory, reality its the same situation. Your flying YWG-YVR-SYD and YWG-YVR clears hypothetically, but YVR-SYD is waitlisted. Previously you would of given up your cert at YWG if you wanted to gamble that YVR-SYD clears. Now you could get some eUpgrade credits back if one clears but not the other, but 15.5 hours of your journey is YVR-SYD, whereas 3 hours gets you to YVR. YWG-YVR is only 20% of your flying time, but you only get 65% of your credits back. (17 taken, -6 for YWG-YVR, 11 given back).
Which will likely leave you just short of being able to upgrade another long haul. It's better than nothing, but likely people will still choose to reject the short upgrade (IE the same thing that happened with paper certs).