I just can’t completely empty the Deleted Items though.
As there is no deleted items showing in your webmail, then will be a local database problem and it needs manual repairing via a dos prompt or terminal prompt.
First close eM Client.
Then if you have Windows see @Gary post in the following thread.
If you have a Mac do the following.
Close eM Client first and then “open the Terminal app via either Launchpad or Utilities” on the Mac. Then Paste and run the following command.
/Applications/eM\ Client.app/Contents/MacOS/eM\ Client /dbrepair
I updated eM Client from 10.0.30-something to 10.1.40-something and no change.
Lastly if you originally downloaded eM Client via the eM Client page, there is also now “newer eM Client versions available” via the release history page you can update to once fixed.
If you do update, close eM Client before updating. Also make a backup before updating incase you need to restore for any reason via “Menu / Backup”. You can see when the backup is complete in Show Operations via clicking the drop-down on the right of Refresh top left.