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)

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