Sounds like a possible database error.
Try manually repairing the database by doing the following for PC or Mac.
If you have a PC see @Gary post in the following thread link on how to repair the database.
https://forum.emclient.com/t/email-message-that-cannot-be-deleted/86994/2
(To repair eM Client database manually for Mac)
Close eM Client 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