You cannot set the synchronization to be only the new rows. In that the changes are migrated to <database2> from <database1>, so that the tables selected in the comparison will become identical.
SQLDataCompare.exe /server1:<Server1_Name> /server2:<Server2_Name> /database1:<DB1_Name> /database2:<DB2_Name> /username1:<database1 username> /password1:<password> /username2:<database2 username> /password2:<password> /Include:Table:\[Table1_Name\] /Include:\[Table2_Name\] /ignoreidentical /ignoreadditional /sync
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