By default, applications on a single Windows host are mapped to a single business application in the Controller. If needed, you can manually configure the .NET Agent to map different applications on the same Windows host to different business applications in the Controller. To map applications on a single host to a different business application, you need to edit the config.xml file manually. please refer to that documentation link it solved that business need: https://docs.appdynamics.com/display/PRO45/Configure+Multiple+Business+Application+Support+for+.NET
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