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It sounds like a bit of a design issue. Data Compare has an option to disable foreign keys, triggers, and primary keys, and it should do this even if the FK is defined on the table at the other end of the relationship, if this option is set. I'd assume the program is doing this twice because both tables in the relationship are being synchronized.
Does this cause the script to throw an error when it is run on the SQL server?
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Is this a problem because I am using such a complex database?