Editing a boot cd in Windows

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I'm trying to edit the isolinux.cfg in a Linux boot iso from Windows. This will be part of a PowerShell script going forwards, so it needs to be command line, but I need to be able to extract, edit and then output a bootable ISO. I've got mkisofs which can do the packaging but it seems that I don't think I'm extracting all the info from the ISO to repackage into a workable ISO.

Google isn't be useful, any hints or links?
 
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