The view mode may on the other hand be insufficient for users who work with lots of folders in Thunderbird. Why? Because the unread folders view mode offers no hierarchical structure. All folders containing unread messages are displayed on their own as root folders in the listing.

And that is a problem if you have lots of folders configured in the email client, as it may take longer than it should be to locate a specific folder with unread messages. That, and the fact that you may need to scroll down to see all folders with unread messages.

The Thunderbird extension Advanced Unread Folders adds a solution for users of the desktop email client.

The extension adds a new view mode to Thunderbird that displays unread messages in their folder hierarchy.

You can switch folder view modes with a click on the next and previous arrow icons on top of the sidebar.

Advanced Unread Folders comes with options to always show specific folders, even if they do not contain unread messages. The inbox, templates and favorite folders are always shown by default. This behavior can be changed in the extension’s options.

You can disable the default folders from showing up in the unread folder view mode, or add Drafts, Sent and Trash folders to it.

Some users may only want to show special folders for certain accounts. You can do that by adding those folders to the favorites in Thunderbird and enabling favorite folders to be always shown in the unread folders view mode.

Advanced Unread Folders is especially handy for users with a large folder structure. Users who only work with default folders in Thunderbird do not really need the extension, as the default unread folders view mode handles that scenario well already. The extension is compatible with all Mozilla Thunderbird versions from 3.1 on. It can be downloaded from the official Thunderbird extensions gallery.

Open the Thunderbird Application Data folder which is located in your document and settings folder in Windows. Select the appropriate Thunderbird profile if there is more than one and click on Mail in that profile. You get a listing of all your email addresses. If you setup Firefox to have different mail folders for every email address you have to click in the folder of the email address that received (or send) the message. Otherwise Local Folders is the way to go.

The important files are those without extensions (Trash, Sent, Inbox ..) – locate the one that contained the mail(s) that you have deleted or are corrupted (do not show up anymore). Open it in an text editor, you could use notepad2 for instance for this purpose. Some folders might be rather big so choose a text editor that can handle large files. Thunderbird should be closed completely while editing those files.

All mails are basically stored in that file. The important part for us are the lines X-Mozilla-Status which defines a certain state of a message such as Read, Unread or Deleted. Search for the message(s) that you want to recover and edit the X-Mozilla-Status: XXXX line into X-Mozilla-Status: 0000 for unread or X-Mozilla-Status: 0001 for read messages.

Recovered messages will appear at the bottom of the folder and should be there after you startup Thunderbird for the next time. You sometimes have to delete the .msf file to make this work. If you edited the file Trash you would delete the file Trash.msf afterwards if the mails do not re-appear after a new start of Thunderbird.

source (and additional information)