Can you elaborate a bit on the situation and what exactly you're trying to do or copy? What version of Revit are you using?
I tested both Copy and Copy/Paste and the System was maintained. That was in Revit MEP 2012. What version are you running? I know I've seen that behavior before. Did your System Duct just disconnect from Mechanical Equipment?
At the moment I don't have the means to test in 2011, but I do know that the Systems and behavior have improved drastically since then. I remember there being many more flaws and quirks back then.
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