When you synchronize the data sources, bear in mind that some rows may not be synchronized if:
To circumvent a problem, select the Disable DML triggers option in the Data Synchronization Wizard before generating the synchronization script.
If you try to compare tables that have primary keys defined on columns with differing collations, the results might be unpredictable.
The Data Compare for SQL Server tool won’t synchronize data in timestamp columns.
In case the structure of the tables you are synchronizing is not identical, the outcome might be unpredictable.
CLR data types can be stored as string or binary values. By default, Data Compare for SQL Server compares and synchronizes CLR types as string. However, it is recommended to enable the Compare CLR types as binary option in the New Dara Comparison Wizard when comparing large CLR data. Nevertheless, do not set this option for the types that do not inherit OComparable interface.
When you select the Disable primary keys, indexes and unique constraints option in the Data Synchronization Wizard, bear in mind that primary keys, indexes or unique constraints that are selected as comparison keys will not be dropped for the synchronization.