As CyberAngel said, highlight changes on the markup after you have made the change. The engineer should be using red for things to be added, you should highlight with yellow when that change is done. (Colors are only suggestions based on what I have seen over my 20+ years doing this.)
At more than one job, the engineer told me to highlight changes after I'd made them. That way both of us know they were done. You can even use different colors for different types of changes or for different drafters.