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You cannot check in a reference table from the command line when the Model repository is configured for version control. The issue can also apply to other objects under version control, for example a flat file data object.
You cannot create a reference table if the STRICT_READ_PERMISSION_OVERWRITE custom property is set in the domain.
If you enter an audit comment when you add a row to a reference table that contains a column with the name Comments, the application writes the audit comment to the row in the Comments column. The issue arises when you work on the reference table in the Analyst tool.
You do not need to update the search index on the Model repository before you run the infacmd cms purge command to remove unused reference tables from the reference data database. The purge command updates the search index before it purges the unused tables.