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As per oracle documentation -> http://docs.oracle.com/cd/B31104_02/books/RRAdm/RRAdmRM_RemoteConcpts12.html
"The Generate New Database component creates the local database template for a given database schema version. The component reads the database schema definition from the Siebel repository, then creates Siebel tables and indexes in a database template file stored on the Siebel Remote server in the dbtempl subdirectory."
Basically after any changes in schema you should run "Generate New Database" job again. That was the reason why I mentioned about generating it again.