A weird situation is when you can see the databases, its tables and so on from phpmyadmin of the concerned cPanel account or even from the backend, but is actually found missing under the ‘Databases’ section.
This issue occurs due to the lack of mapping of databases. Use these commands to re-create the mapping :
# /usr/local/cpanel/bin/setupdbmap : To recreate the dbusermap
# /scripts/update_db_cache : To recreate DB cache