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I presume you reply to messages via all instead of logging into Seller Central each time? There is a setting in Seller Central which reveals a checkbox at the bottom of the email, similar to what shows if you view the message on Seller Central itself.
I did ask Amazon about this a while back and they said there was no way round it. I just have a couple of preset quick replies which get used along the lines of "no problem, thanks", this gets used a lot. The only time this is no use is when you get an out of office auto response from the customer as you can't reply to it as you would just get another auto response. I find these messages get picked up by Amazon and automatically flagged as "you responded on" so I just delete these ones. Periodically I check the unanswered messages in Amazon seller central so I can mark as no response needed in case any slip through the net but if I'm doing a lot of emails I also have seller central open in another tab as well.