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SQL Server 2005 Datawarehouse DB - Integrity failure caused by NonClustered indexes

Last year I've been working with a data warehouse database (SQL Server 2005) loaded on a daily basis during the nights. Overall database performance is acceptable. However, there is a "known error" ...
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Foreign keys can't be added because they exist but they don't exist!

I have a conundrum. I am re-engineering a sqlserver 2005 database, and in the course of doing so have attempted to correct a simple lookup table flaw between tblUsers, tblUserRoles, and tblRoles (...