The information to the right reflects the overall usage, across all folders (including mail and database), while the information you see listed next to the domain is what is stored in the folders for that domain specifically (most usually is in public_html in that case).
Likely the .zip of your public_html is stored outside of the domain folder during the process. If it is no longer in your account the usage will reflect that, the stats part is not instantaneously updated however.