Hello Nikhil,
Welcome to Atlassian Community!
When a customer replies to a notification and it creates a new ticket instead of adding a comment, it means that the customer doesn't have permission on the ticket.
This usually happens when someone that has permission forward the notification to another customer and the customer replies this forwarded email.
The best option, in this case, is always add the person as a participant on the ticket, so they will receive all notifications and they will be able to reply and add a comment as well.
If you want to allow anyone to have access and add comments to a ticket, you can open your project and allow anyone to create their own accounts.
First, go to Project settings > Customer permissions > "Who can access the portal and send requests to the project?" > "Anyone with an account on xxxxx.atlassian.net".
Also, change "Who can customers share requests with?" to "Any customer or organization, by searching this project".
After changing these settings, click on Save and click on "Change the Global settings" or go to Jira settings > Products > Configuration.
On this page, change the "Can customers create their own accounts?" to "Yes, by signing up or sending a request".
Please, give it a try and let us know how it goes.
Regards,
Angélica
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