When merging 2 tickets, you can prevent the email notification from being sent to customers that ticket has been closed.
While merging tickets in Freshdesk, there is an option to set as Not visible to contact, choosing which, the merge action will not be notified to the customers. This has to be enabled in all the tickets that are being merged into one, i.e., the original ticket as well as the ticket(s) being merged.
You can also edit the content of the note by clicking on Edit note option as shown below:
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