Copy running IIS App Pool with Powershell WebAdministration
Have you tried using appcmd instead?
Update: try a combination of both -
Maybe add doesn't let you both import and specify commands. You could try something like this:
appcmd list appool thing1 /xml > c:\tempfile.xml(Get-Content c:\tempfile.xml).Replace("thing1", "thing2") | Out-File c:\tempfile2.xmlappcmd add apppool /in < c:\tempfile2.xml
You may have to debug that script a bit :)
To export the application pool use %windir%\system32\inetsrv\appcmd list apppool "AppPoolName" /config /xml > D:\AppPoolConfig.xml
Without the /config you're missing all of the settings within the application pool and when you go to import that you're only going to create a new application pool with default application pool settings.