When you synchronize the data sources, some rows may not be synchronized if:

• there are triggers defined on the tables

  If you have a trigger defined on a table that inserts data into another table on INSERT, DELETE, or UPDATE, the data in the tables will change as the synchronization is run, which will cause unpredictable results. To avoid this, select the Disable DML triggers project option before you generate the synchronization script.

• primary keys are defined on columns with differing collations
  If you compare tables that have primary keys defined on columns that have different collations, SQL Data Compare may produce unpredictable results.

• columns contain timestamp data
  SQL Data Compare can't synchronize data in timestamp columns.

• table structures are not identical
  If the structure of the tables you're synchronizing is not identical, SQL Data Compare may produce unpredictable results.

CLR data that wasn't synchronized

Data for CLR types can be stored as string or binary values. When CLR data is compared, SQL Data Compare always compares the binary representations. However, by default, when CLR data is synchronized, SQL Data Compare synchronizes the string representations, because binary formats are not always compatible.

If the binary representations are not compatible, they are always displayed as different even if the string representations are identical. String representations do not always contain the full information about the data, so when the databases are re-compared using the binary representations following synchronization, they may be displayed as different.

If you know that the binary formats are compatible, you can select the project configuration option Transport CLR data types as binary.

This forces SQL Data Compare to synchronize the binary representations.

Primary keys, indexes, or unique constraints that weren't dropped for synchronization

If you select the project configuration option Drop primary keys, indexes, and unique constraints, note that primary keys, indexes or unique constraints that are selected as comparison keys are not dropped for the synchronization.