When a mailbox get corrupt when changes the quota, here is the steps to fix it.
1) Login to your cPanel.
2) Select File Manager.
3) Select Home Directory from File Manager Directory Selection popup.
4) Double click mail from Size column.
5) Double click domain name (ie. domain.com) from Size Column.
6) Double click your email username (ie. user@domain.com).
7) Select maildirsize.
8) Select Delete button from the top menu.
Once you delete it, cPanel will reform for the email account automatically and it should correct the email quota size.