Although rare technological glitches sometimes cause changes to your order to be unsaved, the most common reason that Harvest Box substitutions are not saved is because the number of items in your Harvest Box has exceed the quantity limit for the size you selected.
In the top right corner of the customization window, a substitution tracker will appear that tells you the number of Available Substitutions you have. If the number that appears there is a negative number, you will not be able to submit your order and all of your changes will be lost when you close the window.
The easiest way to make sure this doesn't happen is to make sure your Available Substitutions says zero, and that you have the option to click the Submit button. If the Submit button isn't there, you'll need to revise your box before you can save your changes.
If you'd like to add additional items to your order in addition to the Harvest Box, once you have submitted the changes to your Harvest Box, click Browse Products from your Shopping Cart and add any extra items a la carte.