Issues saving enable/disabled status across scenes

I I am currently having an issue saving the enabled/disabled status for the prefabs across scenes.
I looked for a while and nothing came up on the search.

When I press Apply on a prefab, it dosn’t save most of the object’s status.

Example:
GameObj
-ImportantObj1
–Prefab1
–Prefab2
–Model1
—ModelBody
—ModelMisc
—ModelAttach1
—ModelAttach2
-Obj2
-Obj3

ImportantObj1 and GameObj is fine across scenes.

Sometimes Obj2 and 3 are disabled.

Rarely, prefab1 gets disabled. Now the biggest issue I am having is the model part. ModelAttach1 and ModelAttach2 get disabled a lot. Sometimes, Model1 is disabled and leaves it’s children enabled.
I also tried different methods like saving the models as actual prefabs but that didn’t change anything. I even tried pressing Apply to all the game objects and nothing changed. I’m not sure if the “Apply” (Or apply changes to prefab) button is for something like this.
If there is a better or alternate way to make this work properly, I would appreciate it.

Thanks, Nighthawk

Is anyone else having this issue?

Does anyone have an answer?

Are you talking about enabled/disabled state for components, or active/inactive state for entire GameObjects?

If the latter: I believe that active/inactive state is not saved in prefabs (all objects in prefabs are inactive, and are set active when instantiated into the scene).

It’s the active/in-active state of the prefabs when they are instantiated in the scene… For some reason some of the objects are enabled or disabled.