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The saga of measure arguments is long and treacherous but I think you are ready :-)

Each measure.xml (should) contain arguments computed in Ruby using an empty seed Model (e.g. Model.new). This happens for all the measures in the My Measures directory when you press the "Sync Project Measures With Library" button in the OpenStudio Application or PAT.

When you actually drag a measure into the OpenStudio Application or PAT, measure arguments are computed with the current model or seed model. This populates drop down menus with correct names of objects in your model and other model dependent stuff. These model dependent arguments are not saved to the measure.xml.

So for your issues, make sure to update the measure.xml file for your measures using the OpenStudio Application. You will not be able to get model dependent arguments from the measure.xml (if that is what you are trying to do). However, this will be a feature in the upcoming OpenStudio Command Line Interface. It might be possible to replicate the argument getting features of the OpenStudio Application but it would require embedded a Ruby interpretter in your C# application (which I doubt is worth the effort).