Hi Dheeraj,
From what I understood you want to replicate new data into target without dropping the table deleting the table in target.
If so then you can do following:
1. Stop the replication in LTRS system.
2. Refresh FMS
3. Add required tables in "advance replication settings" through LTRS tcode.
Go to LTRS code and select your configuration.
Add table in "Table settings"
Change the refresh behaviour (use truncate) as per screenshot.
4. Start replication in LTRS.
5. Once again add all the required table for replication.
This will just remove the existing data from target and replicate new data without deleting table in target.
Hope helps !!
Regards
BJ