They’ve got you covered in this post in the General forums:
Upgrading your version of Shadowlands
Upgrading from Any Digital Version to Collector’s Edition
If you purchase any digital copy of Shadowlands (Base, Heroic, or Epic), and then upgrade to the Collector’s Edition in the future, we will automatically credit you the cost of the digital copy in Blizzard Balance - as long as you enter the Collector’s Edition key before a future deadline. When you enter the key from your Collector’s Edition, we will see the original transaction on your account and the credit will be added. We will have details on this deadline when we have more information to share regarding the Collector’s Edition.
Just to be clear, you don’t actually “have” CE on your account until you add the code for it from the box when it arrives.