The directory cache contains a total size and number of items for each folder. The cache values are used whenever possible. Manually removing files will not update the cache so the limits have not been recalculated to account for the removed files. Removing mail files via IMAP is preferrable. You can use the button "Refresh Directory Cache" on the Options tab of the user in the admin console to refresh the directory cache for just this one user. The entire cache is rebuilt once a week to catch up to any changes made outside the system.