When you set up an account for a pre-existing email account, Thunderbird attempts to present all the messages to you. Depending on your POP settings, it may also be deleting messages as it downloads them. In that case, this is just a one-time event. To check your setup, click the menu button in upper right (three short stacked lines), then 'account settings', then 'server settings' for the account. That pane will show how Thunderbird is managing the downloads.