I spoke to Systems Designer Nathan Emmott and he had this to say:
Thank you for the update Joveth.
Just a quick question. Does the same thing apply to those that have unopened lower/upper body boxes?
Yup, players will be covered here. If a player has an unopened lockbox for the pieces, then we will send them an equivalent unopened lockbox for the classic items. If they have an opened lockbox for the pieces, then the replacement items will be placed directly into the opened lockbox.