Try setting afeature type fanouton kml_parent in your DGN writer.Kml_parent is the attribute that holds the folder so you should be able to fanout based on this to keep your folders when you write out.It might take a little tweaking from there if you have a complex folder structure.Here's what it will look like in the writer parameters:
I made some changes to the FMW file and was successful in getting data into the DGN file..The problem now is everything is on the same level.looking at the KMZ in the universal view there are definitely different layers and colors..An example FMW would be helpful to help guide me on breaking the levels out..
Some thoughts and potential issues:
Hope something helps.
Could you share us the Workspace Template FMWT to has a better investigate?
Thanks,
Danilo