If the PNRs are cross-referenced then they shouldn’t be booked separately, but no way of knowing if the computer will try and over-ride.
But now it seems you won’t be eligible for upgrades? Are both adults elite and you were trying for 2 elite+companion upgrades? Or just any two of the four passengers? I’m wondering if there will be a problem if the 2 adults are upgraded and then the 2 kids are technically in a separate cabin.