Hi Frank!

I'm sorry for the response delayed so much, the request somehow fell through the cracks.

Your request is perfectly reasonable -- however, it is doable only in certain cases, for example, when the progress is calculated based on time tracking. In that case, if an issue is mentioned twice in different parts, its weight in the final result is the same. However, if we do resolution-based (0 or 100) individual progress + all issues have the same weight, it won't be possible to eliminate double counting.

As a workaround, I can suggest using Formula column instead of Progress column. It lets you calculate progress, for example, with formula SUM { time_spent } / SUM { time_spent + remaining_estimate }. Note that SUM{} construct by default ignores the duplicates.

Additionally, starting with version 4.5, Structure has additional user interface to highlight duplicates, if that is undesired.

Hope that helps!
Igor