WebDeploy 3.6 prerequisites for Import / Export Web Application slightly changed and more rights need to be given for web management to enable these options again.
Here are the steps to allow it again in Windows Server 2012 R2 (and Windows Server 2016):
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Using Server Manager get to Add Roles and Features.
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Pick ‘Management Service’ under Roles/Web Server/Management Tools
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Either uninstall and reinstall WebDeploy 3.6 or use the Change option and make sure to install the “IIS Deployment Handler” for Web Deploy. This will bring back the Import / Export Web Application option again.
Steps to allow it again in Windows 7:
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Go to Turn Windows features on or off
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Under Web Management Tools -> enable IIS Management Service
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same as above for Windows 2012
(for Windows 10 you will likely need to run a repair installation on WebDeploy before this solution works)