A few customers brought to our attention that when you receive an email from eBay notifying you about new message from user and you reply this email directly from LiveAgent that this reply isn't correctly received by the end user. The problem is that eBay needs to have email headers and subject nicely preserved and this article is going to explain how to achieve that.
You need to log in to your LiveAgent admin panel and go to Configuration->Email->Customer templates where you need to edit the Ticket reply template.
Now from subject remove this part " - [{$conversationCode}]" and under the field with the actual template set quoting to include all messages. So this is what you need to achieve:
Once this is done you should be able to reply eBay notifications from LiveAgent just fine.
Note: If you do not wish to include quotes by default on all your replies than you can create a specific eBay department and under Customer templates create a department specific template for this department only. Afterwards you can use automated rule https://support.liveagent.com/038465-Rules to route all tickets from eBay to that specific department so your special eBay reply template is used only for replies on eBay notifications.