The Orders interface in Store Commander includes a 'Products' panel where you can modify some data related to an order previously selected in the central column.
The totals in the 'Large View' will be updated once you refresh the grid.
The invoice will be up-to-date because the PDF creation takes into account the information stored in the database at the time of the PDF download. The PDF file is not stored nor reused.
Any other changes to an order can be carried out on the PrestaShop page directly accessible in Store Commander, Properties panel: