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The following xml fragment defines a custom key for the pair of table dboHR.EmployeesEMPLOYEES:
<TablePairs>
<Pair>
<LeftObject Name="dboHR.EmployeesEMPLOYEES">
<Key Name="Custom_Key">
<Column>EmployeeID<<Column>EMPLOYEE_ID</Column>
</Key>
</LeftObject>
<RightObject Name="dboHR_COPY.EmployeesEMPLOYEES">
<Key Name="Custom_Key">
<Column>EmployeeID<<Column>EMPLOYEE_ID</Column>
</Key>
</RightObject>
</Pair>
</TablePairs>
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