So I checked my original scene’s publish tree and confirmed that even if my UI items are un-checked, the PublishItem instances the tree contains are still marked as checked and active.
I found that the tasks to be publish are yielded by this generator. It seems that only the UI items are marked as checked and not the PublishItems themselves. I may be wrong, but if not, any ideas on how to implement a method where each UI item’s checked state change is stored in the corresponding PublishItem instance as well?