I came across an issue in which the disk space usage on some email accounts, especially the default email account is not updated in cpanel. I have checked the user mailbox of the default email account via Webmail and noticed nothing there. I have done the followings steps to sort out this issue.
1. Log in to the server via SSH
2. Execute the following script :
/scripts/generate_maildirsize --confirm --allaccounts --verbose cpanelusername
If it doesn't solve the issue then use the following steps
1. Log in to the server via SSH
2. Locate the files email_accounts.yaml and email_accounts.cache under .cpanel directory of the user and rename it to a different name.