If database cache file for the user has not been updated, in that case you will see mysql database size ZERO in cPanel. To fix this issue use following steps.
1. vim /var/cpanel/cpanel.config
here searh: disk_usage_include_sqldbs=0 and change it to 1
disk_usage_include_sqldbs=1
2. Now run following cpanel script,
/script/update_db_cache
Thats all.
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