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It is a well known issues that SPModification only removes entries from the default zone. What are people using as a work around. I'm implementing something and I'd like to know how others are working around this issue.

A: 

Never had to use it (knew the issue tho) and in my book it is a combination of 2 techniques:

1- Opening the web.config based on the SPWebApplication (see AlternateUrls property for additional zones)

SPWebApplication webApp = (SPWebApplication)properties.Parent;
Configuration webconfig = WebConfigurationManager.OpenWebConfiguration("/", webApp.Name);

2- Using good ol' XmlDocument manipulation with XPath and friends

F.Aquino