On the DSM-G600 you only have to set the UPnPAV path to a single folder. I do not think you can set it to multiple folders (that would not make sense).
This folder should be the root for all of your media. This does not mean the folder has to exist at the root of the hard drive. You can point to a sub folder on the hard drive and all of the folders that are below will contain your media and be refreshed when you select refresh.
What I do is create a folder called UPnPAV and then create three folders called Music, Video and Photo in the UPnPAV folder. In the music, video and photo folders I create folders that catagorize the media such a artists, albums, photo albums etc.. In all I have 5245 files in 674 folders occupying 207 GB of space. This file sytem works all the time. When I add media I refresh the UPnPAV folder succesfully everytime.
Never had a problem with the refresh. I have ripped .wav files into these folder using WMP11 without any problem (had to delete the junk files that WMP11 puts there that are not music). The folders refreshed fine even with the junk files.
I have had mixed succes using D-links phone support. Thier email support and this forum seem to be OK. I rate the DSM-G600 as a pretty good media server to use with the DSM 520. I would not worry about D-link deleting your post. They put up with worst crtiicism and seem to handle it very well.