@SatyaSDasika1 yes, absolutely. An email reply generated OOTB/CS email channel adds a ET- or I- case ids in subject line which helps maintain the chaining. Does that answer your question? Please post if you have follow up questions.
@Vikas@Multichannel : This is if the email is triggered from Pega. What if, the email comes into the email box from an external user. Can we track them together, there is no headlines or case information in them.
We generally don't rely on custom email headers to tie the email threads together because email clients remove custom headers. Case ID needs to be present in subject line (OOTB with email channel) or encrypted within body (coming up soon)