This shouldn't happen, therefore something is wrong.

Who is the mail provider?

Lycos Mail. Lycos Mail is changing their 3GB free email quota to 500MB. So I'm planning to move all of my Lycos Mail folders to to my Lycos Mail inbox and bring it all down as POP (not IMAP). I'm presently conducting a test or tests to see how it all works. (I've never used a PC based email client before - only web based.) 9/30/16 is when Lycos Mail changes my 2 free accounts to 500MB and turns off POP and IMAP for free accounts too. This morning I had 6 dups which were easy enough to delete. But I was just wondering why the dups occurred. Thanks for getting back to me.

Sounds like it's time to find a better email provider. Lycos would appear to be backing out of this market, or else trying to persuade you to take up a paid-for, subscription-based account.

If you have a folder structure in webmail, IMAP would be a better tool for accessing your folder system. Just copy or move everything to Local Folders (or an alternative email account).

POP can "see" only your Inbox, so you'll have a laborious procedure of moving messages into the Inbox to make them visible to Thunderbird, and then reconstructing your folder system.

You may find that Lycos will allow you to forward messages to another account, and another email provider will allow you to register the email address provided by Lycos, allowing you to continue receiving and sending email using the Lycos account identity.

Hi. I'm going with POP. I need to retain 5 years of emails. With IMAP my Thunderbird emails will be deleted when I bring my Lycos Mail account down to 500MB. Moving my folders to my inbox will be easy. I will be able to sort out and organize my emails within the Thunderbird POP environment. I'm presently forwarding my Lycos Mail to Gmail. Can you think of anything on the dups?

I have this problem too. With hotmail. Please see:

https://support.mozilla.org/en-US/questions/1061656

and

https://support.mozilla.org/en-US/questions/1005565

I am about to make another post about this too.