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
• (For MS Store version of eM Client the command is eMClientStore.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.