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Normally, it should not delete the email, I think there is a configuration issue. Please delete the yahoo account from Thunderbird and restart the system and now follow the procedure listed here in sequence:

1 aunch a Web browser.
2Navigate to the WebMail download page (see Resources).
3Right-click on the WebMail and Yahoo! extension files and select "Save Link As" to store the extension files on your computer.
4Launch Thunderbird.
5Select "Tools" and then "Add-ons."
6Click the "Install" button at the bottom left.
7Select the WebMail extension file you downloaded earlier and then repeat the installation steps for the Yahoo! extension.
8Restart Thunderbird.
9Select "File," "New" and then "Other Accounts."
10Select "Web Mail" and then click "Next."
11Type your name and Yahoo! Mail address and then click "Next."
12Type your full Yahoo! Mail address (including "@yahoo.com") as your user name and then click "Next."
13Click "Finish" to complete the account setup and then restart Thunderbird.
14Enter your Yahoo! Mail password when Thunderbird launches to validate your account. You can optionally choose to have Thunderbird remember your password. Your messages will now be downloaded and you can begin using Thunderbird with your account.

Here’s to Good Karma