Not finding the mailboxes that you have meticulously organized can be frustrating. Mac Mail will allow you to Hide the folders the mail is in and if you do not know how to Show the folders they will be “lost” to you.
Open Mac Mail and roll your mouse over the name of your mail. For example, you import Gmail into your Mac Mail account. Roll the mouse over Google, (or Gmail), and you will see a plus sign (+) or the term Show. Click the term Show to show all the folders within Google. Or Hide to re-hide them. Clicking the plus sign will allow you to create a new folder within that file structure but will NOT allow you to Show or Hide the folders.