Response time calculations are based on difference between the response and the previous message. That means even within the same conversation, each reply (back to the customer) is calculated and factored into the average. The calculation also only takes place if previous message is from customer and in an "Unresolved" state. If either the previous message is from a staff or if the conversation is closed, Reamaze will stop calculate response times.
If you need to wait a long time since the last customer reply to follow up, you can pause response times by adding an internal note or setting a reminder on the conversation.