Removing meals from a day's menu (individually via the portion selector, or all at once with Clear Menu) only deletes the menu lines and their Quantity Needed for that date. On-hand stock is a separate, dated-independent figure that only changes through stock movements. If meals were already added to stock with Update Stock and you no longer want them counted, record a Remove Stock movement in Stock Management with an appropriate reason, or undo the CSV upload if that is how the stock was added.