Hi Dan, sorry for the delay, I was out os office.

I usually do this kind of stuff into the proxy method:

• Search with a regex expression or xpath all occurrence of old references in the legacy umbraco.config.
• Get the new Id of the reference in the new Umbraco cache. The legacy nodeId is supposed to be stored into a property in the new instance for the mirroring.
• Update de XML source of  uMirror with the new nodeId.

Example for an umbracoRedirect property, not exactly your case but similar:

/***************************************************/
/* Read the legacy umbraco.config */
/***************************************************/
string SourceFilePath = HttpContext.Current.Server.MapPath("\\App_Data\\umirror\\umbraco.config");
string umbracoconfig = System.IO.File.ReadAllText(SourceFilePath);
XDocument xml = XDocument.Parse(umbracoconfig);

/***************************************************/
/* Get umbraco content */
/***************************************************/
XmlDocument XmlContent = ((XmlDocument)content.Instance.XmlContent.Clone());

/***************************************************/
/* Update value */
/***************************************************/
foreach (XElement index in xml.XPathSelectElements("//umbracoRedirect").Where(r => !string.IsNullOrEmpty(r.Value)).ToList())
{
            if (XmlContent.SelectSingleNode("//* [legacyId = " + index.Value + "]") != null)
                index.Value = XmlContent.SelectSingleNode("//* [legacyId = " + index.Value + "]").Attributes["id"].Value;
}

...