I recently updated by Thunderbird to the latest version 52.3.0 last week. Since then, any email that I reply from Thunderbird via POP3 it downloads back to Inbox. The copy is not saved in the Sent items. Also, the email is showing up in my sent folder via web-mail service. I checked with my service provider, they said that it has to do something with the recent update from Thunderbird which changed the behavior. I too suspect the same. Currently, I have set a message filter rule to move all my sent emails to Sent Items (Thunderbird) from Inbox. My Copy & Folder settings are set to save emails in my web-server account.