Recently, I noticed an issue with cPanel and mail quotas. The problem was, cPanel was showing that an account was over quota when there was actually no mail.

This issue stems from a rare issue with corrupt maildirsize files. The fix is simple and just requires this command being run:

# /scripts/generate_maildirsize --confirm [account_name]

That will regenerate maildirsize and will instantly recalculate the amount of mail in an account thus rectifing the false report of it being over quota.

The reason this corrupt maildirsize is such an issue is that cPanel will think that the account is over quota and therefore reject mail coming in for that account.