If you carn’t delete or move the message and closing and reopening eM Client and rebooting your computer also makes no difference, and that message “does not appear online in your mailbox”, then try closing eM Client and running the database repair manually via the Command prompt or Terminal. See my post below.
However if that message is showing in the same place online via webmail, then “close eM Client” and delete the message online, and then reopen eM Client which should then remove it locally when eM Client recconects / syncs.
Alternatively if you have been making regular eM Client backups either automatically via the Settings or manually via the Menu, then you can instead try restoring your last recent backup via “Menu / File / Restore” when you didn’t have that message problem & continue on from there.