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you should move your config store and arcgis server directories to D. I am afraid you installed ArcGIS Server on an EC2 instance on your own. It is good practice to get ArcGIS for Server AMIs from Esri Customer Service and setup your GIS Servers in Amazon by launching these AMIs. The Esri AMIs are configured to take things like this into account.
I especulate that your c:/arcgisserver folder is growing because either your logs are growing (you can configure clean up policies from Manager), or because you are publishing service definitions that include data.