This is an interesting issue with cPanel recently faced by one of my clients. Searching on the internet brings me to an article in cPanel forum where someone else happens to also face such an issue. The solution is pretty straight forward firing the below command with the email affected.
doveadm force-resync -u [email protected] INBOX
It seems like the inbox just needed a re-sync rather than the user third party email got deleted. This guy definitely save my ass!