I have found that sometimes when replying to JIRA emails as a reporter the responses are not added as comments. I assume there are some kind of permission issues here. When I reply to an email it always gets added, however, when I try from a test account with customer only permissions it does not work.
What determines that this is possible?
When you open the project settings and go to "Email requests", do you see that email requests are enabled? Email requests need to be turned in order to receive comments from customers.
If this turns out to be your problem, but you don't want to receive new requests via email, here's the workaround that Atlassian support suggested and that we're using:
Configure an Automation rule to automatically resolve requests that come in via the email channel, after having added a comment referring your users to the Customer Portal. You can extend this using an add-on to go so far as to delete the requests that come in via email if having them lingering resolved is undesirable.
There's also a feature request to separate new email requests from comments via email, but it doesn't seem to be high priority. :)
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