I am sure that HtmlUtility and AntiXss (another MS URL encoding tool) will not help here. A "." in the URL is considered valid and therefore it does not need to be encoded.
I think you will have to publish your own encoded string to further encode other characters that are not valid in the Google webmasters APIs.
i.e. do something like that ...
var encodedUrl = HttpUtility.UrlEncode("http://www.example.com") .Replace(".", "%2E");
... assuming "." this is the only character you have encountered.
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