Hello Lior,
For our Service Desk email handling we use the Email Handling function associated with Service Desk. It looks like you are using the general purpose email handler for JIRA Software.
Here's the documentation link for the JIRA Service Desk email handler:
https://support.atlassian.com/jira-service-desk-cloud/docs/receive-requests-from-an-email-address/
Additionally, we simply set Strip Quotes to True, and that seems to take care of excluding everything below the "reply above this line" in the email.
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I found an article for JIRA Server that talks about various methods to strip the original content from a reply:
Perhaps one of those methods will work better for you.
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