cPanel quotas aren't updated in real time. If you delete a large file, or a number of files that should have made an impact on the overall disc space, it will take a while to show up in cPanel on the 'disc space used' graph.
You can force an update by opening cPanel and clicking on the 'Disk space usage' icon under the "Files" category. Click that, look at the resulting page, then when you return to the cpanel home page it should reflect the new amount used. If not, refreshing the page will show the updated numbers.