Resending webform submission doesn't use custom mail template
Site was using two different themes and webform was submitted from the front end theme(first theme) and back end theme(second theme)
The problem was that the webform template was present in the front end theme and not in the back end theme. So that's why when the user submitted the webform once the email uses the custom template.and when the user edit the webform under the back end theme the webform custom template is not present in this theme so the webform was using the default template.
Fix : Keep the similar custom template in both themes.