Hello Danish,
Thank you for providing the details around your issue.
If I understand correctly, you are currently using Server-Side Sync to track emails to Dynamics 365. However, you are wondering if there is a way to only track the latest reply and not the entire thread.
With what I believe you are trying to accomplish, the answer would be no we cannot just track the latest reply and not track the entire email.
With Server-Side Sync, we are synchronizing a user's exchange mailbox that we have enabled in Dynamics 365. If the user manually tracks an email from their Exchange Inbox or if the email meets the criteria to automatically be promoted, we make a request to create that activity (via Server Side Sync) in Dynamics 365.
Server-Side Sync is just taking the details for the email and creating a mirror image of that email in Dynamics 365. From what you are describing, you would like to track on the latest reply into Dynamics 365 from that email which SSS is not able to perform at this time.
Please correct me if my assumptions are incorrect.
Thanks,
Lance Koplin
Microsoft Dynamics 365
Support Engineer