This scenario typically comes up when a customer has already received some of the items in their Sales Order and are requesting a change to the items they are ordering.
In this case you can close the Sales Order - that resets the non-shipped quantities of the products included in this Sales Order to zero.
You can then clone the Sales Order (using the Clone Sales Order option) to create a new version of the existing Sales Order.
The new -cloned- Sales Order will be created in Pending status so, you'll be able to update anything you want such as remove or add rows, update quantities, change prices etc. Then, you can verify the sales order and continue as usual.
A similar process can be applied for Purchase Orders.