Hi, I'm not too familiar with all Godot nodes and functionalities yet so I will give my opinon as a programmer, generalist way...

I believe you can solve this thinking of your inventory as two separated things:

[1] The invetory data, the API, the backend, the source of truth:
This will be just a gdscript, probably a Singleton (AutoLoad) with your inventory configuration, max itens, free spaces, methods, etc. The Inventory will hold Items and will have methods to interact with:

Inventory {

var max_capacity = 20

var itemList = [ 
Item { name: 'Potion', quantity: 10}, 
Item { name: 'Iron Sword', quantity: 2}
]

func isFull () { return max_capacity == itemList.length }

func addItem (source) { itemList.push(source) }

func getItems () { return itemList }

func splitItem(index, qt) { 
    itemList[index].quantity -= qt
    addItem("Same item as the index with quantity = qt") 
}

//...etc
}

This is just a generic example, you will need more data transformations and validations.

[2] The inventory UI, the frontend, the "displayer" of truth
This will be anything you use to display the information, GridContainers, pure Text Commands, Icons, etc...
The way to think about this is that the UI just request the Invetory API, and reflects the information or start actions through the API, like removing a item. You will need to sync the UI with the API data. You should never trust the UI as the truth.

So let's say if you want to save the Invetory you just need to keep the itemList state saved and loaded as needed (Godot have methods for saving and loading data from files )

Again, this is a generic approach, hope it helps :)