My experience is that upgrades on international flights frequently do not clear in advance. More so an issue with the reconfigured aircraft, which have smaller premium cabins. Other than not being able to choose a preferred seat, it has not been a huge deal to me since 1Ks almost always clear at the gate. [I have been a 1K for the past 12-years and have only had one international upgrade not clear--that was from C to F from BKK to NRT.]

This could be an issue for you, however, because, at the gate, each person clears based on their own status. So while you will almost certainly clear, your two-year-old will not be a 1K and very well may not.