When you synchronize the data sources, bear in mind that some rows may not be synchronized if:
To work around the issue, select the Disable DML triggers option in the Data Synchronization Wizard before generating a synchronization script.
If you try to compare tables that have primary keys defined on columns with different collations, the results might be unpredictable.
In case the structure of the tables you are synchronizing is not identical, the outcome might be unpredictable.
When you select the Disable primary keys and indexes 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.