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I have a PowerShell script that creates a web application using New-SPWebApplication. It crashed for some reason a while back and now it keeps telling me the application pool exists. I've looked in IIS, in SharePoint Central Administration -> Web Applications and using PowerShell Get-SPServiceApplicationPool, but cannot find it anywhere. It seems that SharePoint has convinced itself the application pool is present, but I'm unable to remove it and start over.

Is there a way to persuade SharePoint that the application pool does not in fact exist so I can recreate the web application?

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I've solved it. Needed to run the following code to unprovision the offending application pools:

var pool = Microsoft.SharePoint.Administration.SPWebService.ContentService.ApplicationPools["[Name of pool]"];
pool.UnprovisionGlobally();

This removed the application pool from SharePoint allowing me to recreate the web application.

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