Yep, it'll work just fine; I did that to upgrade my PS4 license. However, it's worth noting that in my experience it may make you try to register the base game/HW/Stormblood to an account, which can complicate the upgrade.

In my case, it registered Shadowbringers PS4 to my account and then promptly errored out with a complaint that it couldn't register the PS4 versions of ARR/HW/Stormblood because I already had those licenses. I just told it to make a second service account (on the same login), and then it was happy and finished the upgrade. Yeah, this meant I ended up with a second service account that has PS4 licenses for ARR/HW/Stormblood on the same login, and if I go to the 'Data Center' option at the main menu on PS4 it asks first which service account I want to use before letting me pick data center, but I can just always pick Service Account 1 and ignore Service Account 2.