Per tech support headers are only stored for 1 week, so Freshdesk is unable to thread messages sent after 1 week. So if a customer sends an email creating a case, we ask a question, and the customer responds 8 days later there response will fork a new case and we will have to merge them. We do this a lot… A simple fix is for Freshdesk to follow RFC standards and keep headers for threading in their DB as we wouldn’t need to merge cases if they did this.
The recommended work around was to modify the subject, but our Marketing team would not approve such a change as it would confuse our customers if we started changing subjects to add a case ID to work around Freshdesk shortcoming(not storing headers for more than 1 week).