What do you have in your server settings for the locations marked in red in the image?

If you have a POP mail account:

To download emails to Thunderbird and keep emails on server and delete after eg: month (helpful in case of backup) , but if you manually delete email then delete off server before waiting a month.

• Right click on pop mail account name in Folder Pane and select 'Settings'.
• Select 'Server Settings' for pop mail account
• Select: 'check for new messages at startup'
• Select 'check for new messages every eg: 10 minutes'
• Select 'automatically download new messages'

• Select: 'Leave messages on server'
• Select: 'For at most 30 days'
• Select: 'Until I delete them'
• click on 'OK'

Suggest you close thunderbird, wait a few moments for background processes to complete and then start Thunderbird.

Please note: After deleteing emails in pop mail account Inbox, the deleted emails appear to go to the 'Deleted'/'Trash' folder, but in really they are 'marked as deleted' and hidden from the Inbox view, but still remain in the Inbox mbox file. Compacting the Inbox will remove the 'deleted' emails and then they will be deleted off server. Right click on Inbox and select 'Compact'.

I have discovered that if I use 'Message Filters' to have some emails filtered to another folder, when I delete those emails, they are not deleted off server some some unknown reason. To get around this, I have set an action in the filter to move to folder and then remove it of the pop server.

This still didn't work. I had it delete off the server after two days, but the only one it did not delete was one (1) of them from yesterday!

Otherwise, I followed exactly the steps you suggested.

Thanks, but ??