I am having a similar problem. I added custom properties to several shapes in a VSDX file via code (using aspose.diagram for java). I am trying to save the VSDX file as a SVG. the code saves the SVG file and the file loads in my app. When I look into the SVG file, none of the custom properties got saved. I lopened the saved VSDX file in Visio and verified that all the custom properties are in fact in the diagram. Manually exporting from Visio saves the SVG correctly but it seems saving from does does not fully work.
It seems like you’re using Aspose.Diagram downloadable API. Which one are you using .NET or Java? Also, I’ll have to move your query to Aspose.Diagram forum at forum.aspose.com so our support team can help you properly.