Eu acabei usando o msdeploy:
Exportar:
C:\Program Files\IIS\Microsoft Web Deploy V3>msdeploy.exe -verb:sync -source:apphostconfig="myWebSite" -enableLink:AppPoolExtension -dest:archivedir=c:\NavProd.zip,encryptPassword=myPassWord > wdPackage.log
Importar:
C:\Program Files\IIS\Microsoft Web Deploy V3>msdeploy.exe -verb:sync -source:archivedir=c:\myWebSite.zip,encryptPassword=myPassWord -enableLink:AppPoolExtension - dest:apphostconfig="myWebSite" > wddeploy.log