Hello,
There are some issues related to the email chain stability.
As i know it is related to the subject.
Some customers had no issues when we worked on zendesk, now each customer's new answer it is like a new conversation ticket. We have raised this question to your support but the answer was that it is a problem with the customer's email client.
Also if it is related to the subject it has issues with sending answers to conversations converted to tickets where conversation start on chat but going via email- all tickets has ticket subject like “Ticket”