Why are the variables not clearing in the OpenStudio idf file?

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I am using OpenStudio 2.5.0 for a project. I selected some variables to view, and successfully ran the osm file. I then changed the specific variables and frequencies of report. Ran the osm file and in viewing the variable output file in csv format, I noticed that the variables I had deleted were still present, one of which was mistakenly selected as time step. I opened up the OpenStudio generated idf file and discovered that the variables I had deleted were still in the idf file. I then manually deleted the offending variables and ran the idf file in EnergyPlus. Why are they not clearing in OpenStudio? Actually I have noticed this happening when changing the parameters in an outdoor air object.

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Thank you Avi for raising this issue. I have also found that removed objects in HVAC loops appear not to be deleted also and causing program runtime failure. I have had to run OpenStudio again with ideal loads selected to "clear" the loop then rebuild the loop.