Hi Javier,
WHMCS will automatically trim emails after a breakline. These are defined in the tblticketbreaklines table.
You must be getting emails from customers without a breakline or in a different format.

You can add the particular break line being used by the customer in question as a new row to the tblticketbreaklines table.
One other option would be to add a breakline to the top of the Support Ticket Reply email template, to direct clients to top-reply:

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