In order to adjust a submitted sales order, there are two ways to do it:
1 – In order to close all remaining items, click on the Status button and click on “Close”. This will close all remaining items and the sales order will be finished.
2 – If items need to be added or less than all the remaining items need to be removed, than you click on the “remaining Items” button, and adjust the quantity of each item to the new desired quantity, and ad new items if needed.
My forum discussion explains this very well:
https://discuss.frappe.io/t/submitted-sales-order/95450
Sales order – remove or add items after submitting