This happens due to may reasons like MySql service is not running or Perl modules may get corrupted, You need to check the /var/lib/MySql folder to check the database names are not named incorrectly, if you find that all the names are proper and all the databases are under MySql user. Then run to following command :
Quote:
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/scripts/update_db_cache *
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It will map the database with particular user account and you would see the databases in cpanel.