How to separate automatically populated tables from manually populated tables, properly, in SQL Server?

I'd suggest you use an import table that gets updated by the service and then populate the movies tables from that. Then you get to keep movies that are deleted in the movies table. Possible tagging them as deleted or obsolete, but you'd still be able to keep them for historical purposes.

I think you should use a soft delete for that scenario. I don't think you want to have comments you don't know which movie they belong to.

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