You can choose to save the database structure to a snapshot file before comparing and synchronizing the database schema. To do this, check "Take a snapshot of the database before synchronization" and specify a snapshot file.
Below is the xml fragment generated when you choose to save the database to a snapshot file.
<LeftDatabase>
<SqlServer>DEVSRV002\SQL2016</SqlServer>
<DatabaseName>AdventureWorks</DatabaseName>
<TrustedConnection>true</TrustedConnection>
<SaveToSnapshotFile>D:\QA\xSQL\SqlSchema\Snapshots\AdvWorks.snpx</SaveToSnapshotFile>
</LeftDatabase>
<RightDatabase>
<SqlServer>DEVSRV003\SQL2019</SqlServer>
<DatabaseName>AdventureWorks</DatabaseName>
<TrustedConnection>true</TrustedConnection>
</RightDatabase>