If a customer ignores the message that says "reply above this line" but, instead, replies inline, the agent cannot see anything of the reply.

In competing platforms that behave in a similar way (<cough> Zendesk), there is a link that allows the agent to still see the complete original email so that the inline text can be retrieved.

Please consider adding such functionality as that would avoid the need to go back to the customer and ask them to reply again.