Did you send this new envelope using a Template or just using "Send an Envelope"? In either case make sure the Branding dropdown is set to the correct "brand" you just created. Each new envelope has Advanced Options and has a dropdown called Branding and would grab the default Brand each time a new envelope was created. If using a Template however the Branding was set at whatever the default was at the time of Template creation so you may need to edit the Template and adjust the Advanced Options and Save.

While using that template for sending, It asks for recipients and further advanced options. So during sending I did change the option of branding to the one I had modified, it did change the logo in the email template which I sent to the user so branding worked, but however the xml change which I had applied inside the email resource file did not get affected.

Perhaps the XML you uploaded did not get saved or possibly a syntax error. I would suggest downloading the XML and checking the file for the change. DocuSign does note in articles that these XML can get reset back to defaults. Outside of checking the XML and possibly re-uploading, I would create a DocuSign Support case so they can review those changes.

Attached is the XML file which I did upload for the Email Resource. In that I had replaced the HTML content of  DigitalSignaturesPending_HTMLBody section.

If you can help me out in finding the issue it would be a great help.

Thanks. @David Schmitz​ 

So based on the section you modified this email is sent at the time a "Digital" signature is required on the envelope. Is this what you are expecting? In your initial post you mention "I want to customize the Email template which is sent to the user to sign the document." which to me reads like "customize the message Recipients see when signing electronically", which is different from a Digital signature. Perhaps you used those words interchangeably or more likely I think the area you modified might not be affecting the email you are expecting.

Yes David, you got it right. I want to modify the template of this email which the user gets to click the review document and sign. Can you let me know If I am changing the template at the correct position or not? And If you can also let me know whether I am wrong at updating the XML or is it the syntax errors?

So I re-reviewed the Email Resource file and the section that you modified must be the correct time as I see no other reference to an email that is similar to the email received by Recipients. However as you noted you do not see the changes so this is either the wrong area r there is a syntax. Have you tried reverting back to the original file and then making a very small text change?

I would suggest opening a DocuSign case if you do not have access to the original file or need greater details on the exact section to modify in the resource file as it looks accurate to me.