Actually, it wouldn't be.
You would need to enter the SQ FF number, leave that until upgrade, and then change to VA FF number once the upgrade is done (I'm assuming there are no issues doing this.)
This is the message about upgrading with miles you get with a Velocity number entered "Your booking cannot be upgraded. Online redemption upgrades can only be made if passenger names in the booking match the names of the KrisFlyer member or his/her redemption nominees"