Emails come from your Inbox on your providers server. Go to their web mail page and log into your account. Read and delete the problem email. If you need to keep it move it to a different folder from the Inbox.

I have the same problem. I went to the webmail page of my mail provider, and the email isn't there. I closed Thunderbird so that if the message is in my provider, it won't automatically download to Thunderbird before I can delete it. But it isn't there.

It has to go THROUGH the provider's hands before it can get to Thunderbird, but the email has already gone through. As far as my provider is concerned, there's no mail in the inbox.

I'm missing a few hundred emails because of this! Can any one help me?