When you save a custom theme, you are saving a template that can be used to apply to your forms. If you change the theme manually and save a new custom theme or save over an existing custom theme, the saved template updates, but it doesn't touch any of the forms. A process designer needs to go and re-apply the custom theme for the changes to take affect. 

This is done because not all users have access to modify all processes. If you have a user that is given process admin rights to a single process, they'd have the ability to save over a custom theme and change all the other forms that use it. This might break other forms that the user shouldn't have had access to.