Is there any way to configure the JIRA to update tickets when the email comes with same subject in the email handler without using ticket number in the subject ?
No, it relies on the issue number (the summary is not unique, so you can't really use it as a simple match)
You'll need your own mail handler to do that (one that can cope with non-unique strings, and encapsulates your logic on matching - e.g. if the email has a valid issue id, and a valid summary that matches a different issue)
Nic is right, JIRA cannot do it for you. You either develop your own mail handler, or use Email This Issue a JIRA add-on that can do this for you.
If you need more information on how exactly it works, please let me know.
Tibor
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