For whatever reason, any time an issue is marked as 'in progress' or 'closed', it gets taken out of my portfolio.
@alexaadkins , Are you using a filter as source of your plan?
It could be due to the filter you are using in your portfolio plan. if your filter avoids in-progress and closed statuses in some point this will affects your portfolio plan as well.
can you please share the filter , If you are using a filter as plan source ?
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