Putting messages back on a POP3 server

tools -> account settings -> server settings -> leave messages on server controls whether a copy of the message is left on the POP3 server after Thunderbird downloads a new message. If you checkmark this setting you will still be able to read the message from webmail after reading the message in Thunderbird. Its disabled by default.

This can cause a problem if you didn't notice the setting. If you want to put a copy of your messages back on the POP3 server so that you can see them from webmail you could forward the messages to yourself. However, that would add new headers. A better solution would be to install the mailredirect extension and use it to redirect the messages to yourself. That essentially forwards the message while making all of the important headers look like the headers in the original message.