Please try the following steps to get rid of any 'ghost' messages:
- Turn off Conversations (Menu > View > Conversations > Disable Conversations)
- Close eM Client
- Open RUN function from the Start menu
- Run the command ""C:\Program Files (x86)\eM Client\MailClient.exe"" /dbrepair
- Wait until the database check is completed
- Turn eM Client on
- You should then be able to set any Conversations setting you prefer.
For IMAP and Exchange accounts only:
- If that doesn't help, please right-click on the folder that the messages are in, select Properties > Repair and click the Repair button.
- This will prompt the resynchronization of this folder from the server and should reset its data.
- You can also try removing your account from eM Client and then adding it again in Menu > Accounts.
Please note that all locally stored data will be lost, but if you have your data on the server, that shouldn't be of concern.
You can make a backup just to be on the safe side through Menu > Backup.