Suddenly I found that all configuration and Database has been deleted

The hsql database files are found in the tomcat subdirectory of the install by default. (e.g. /opt/ccollab_server/tomcat); user information is stored in the embedded DB as well.  There is an automated DB backup feature, but I am not sure off hand if it is enabled for the free version.  Those are stored as daily snapshots in tar.gz format in tomcat/collaborator-content-cache/db_backups; sadly if your database is corrupted and has been for longer than seven days then it is likely those backup files are themselves storing incorrect information.