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Can you also check if the min_valid_version of the table is less then or equal to the currentVersion?

i.e. min_valid_version from sys.change_tracking_tables t where t.object_id = object_id(%tableName) <= select change_tracking_current_version()

Also, You can also modify the log level to "DEBUG" to check if the tables are selected or not: https://streamsets.com/documentation/datacollector/latest/help/#Administration/Administration_title.html