You could add a reference to the flowchart.net.dll to your project, and do the following:

MindFusion.FlowChartX.FlowChart fc = MindFusion.FlowChartX.FlowChart();
fc.LoadFromString(myWebChart.SaveToString());

VisioExport visio = new VisioExporter();
visio.TemplatePath = "path to the VisioExport.vxt file";
visio.Export(fc, "path to the .vdx file");

The Webchart and Flowchart.NET dlls are the same, only the Windows Forms references are removed from the former. We created Webchart because ASP.NET 1.0 could not work well with Windows Forms controls. Now ASP.NET 1.1 and 2.0 don't have any problems with Windows Forms, so you can stop using the Webchart.dll assembly altogether and just use the Flowchart.NET one.

Webchart.dll still runs a bit faster and requires fewer resources on the server, because ASP.NET loads WinForms assemblies in a new application domain, and runs a message queue for each WinForms control loaded.

Stoyan