Hi Shailesh Jain,
There is no truncate option for MSDCRM target like we have for Relational targets like Oracle.
Below design can be used:
1) Create a mapping to read data from MSDCRM source and write to flatfile target. Connect only Primary key in the flatfile target.
2) Create another mapping with flatfile(generated by mapping one) as source and MSDCRM target. In the session properties, select 'Treat source rows as' option as 'Delete'.