If no new scenarios have been generated, the Update icon will be grayed out. After you update a model, the Update icon will be grayed out.
You can access this from the main menu, on right-mouse-click and with a keyboard shortcut:
In the Optimization menu, use the save icon to reflect your changes (new scenarios with optimized factor settings) in your Excel file or Reaction Lab model.
To save these changes to disk, you should use File>Save in Excel or Reaction Lab.
It is common to run a full factorial exploration using an Optimization scenario as the centre-point / base case; this helps to determine whether the optimum is a sharp 'cliff edge' or a relative flat 'plateau' that is more robust to small changes in factor settings.