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Thanks for your post.
There is a project option to ignore constraints and indexes, but they don't get ignored when the database is deployed.
There is an option with SQL Data Compare that forces the constraints to be enabled with NOCHECK. This would mean you could also deploy the constraints, but the existing data won't be validated against the constraint when it gets created. This might be helpful, unless you actually want the constraints to be different.
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ie:(/Exclude:storedprocedure:proc_thisproc)