Thunderbird 3 – leave messages on server option

1. Go to Options -> Advanced -> Config Editor.

2. Find the Name mail . pop3 . deleteFromServerOnMove

3. Set it to True.

True: Delete the copy of the message on the POP3 server if you move or delete the message.

False(default): Only delete the copy of the message on the POP3 server if you delete the message.

That's it, restart Thunderbird. You need to press 'Get Mail' everytime you want to sync with the email server, in order for you to make sure messages in the application is in sync with the email server.

The following should be emphasized to realize the sync with the server. You will not see your server message disappear upon the initial Get Mail download (new messages downloaded). After you process your Inbox in Thunderbird by deleting/moving a new message, then do another Get Mail which will delete the new messages previously downloaded on the server (put in sync).

Note: If you have older messages in your Thunderbird Inbox, they will not be deleted from Server. Delete them manually from server. From then on, any new messages you download, then process (delete/move), and then do the sync by doing Get Mail again WILL be deleted.

The Email Address Crawler Plugin might work. Note that the earlier version is no longer maintained. To use the updated version:

1. Follow the direct download link. (Attention this is not approved by Mozila jet, see comment below)
2. Start Thunderbird (v31.0 or greater).
3. Open the triple-bar menu (≡).
4. Click Add-ons.
5. Click the icon beside the search text box to open a drop-down menu.
6. Select Install Add-on From File...*
7. Browse to the download location for Email Crawler.
8. Select the file (e.g., emailcrawler-5.1.2.xpi).
9. Click Open.
10. Click Install Now.
11. Click Restart Now.

Then:

1. Right-click on any folder.
2. Select Crawl folder for email addresses.
3. Check To and From.
4. Set Choose a [sic] addressbook as a target for the found addresses to Collected Addresses.
5. Optionally, set Needed # of occurrences to 2 (to help filter invalid addresses).
6. Click OK.

If you want to use an approved Plugin from Moxilla Add-On Page, maybe the Email Address Crawler Plugin is a solution for you?

EMail Address Crawler by CySlider
Automatically fill your address books or send mass mails with e-mail addresses extracted from all your e-mails.

It is a bit outdated, but there is stated by someone it that still worked in 17.0, so maybe it still works in Thunderbird 31