I don’t thinking mapping deeper in the directory structure is going to help you because the path length is based on the depth from the drive letter (on the server, not the client mapped drive). I doubt there is anything you can do with it in VB since it’s an OS problem.
The ways I know of getting around this problem are to use Xcopy /C (continue if error occurs) to copy across what will go and locally copy the other files to another media on the server. This will have to be manually moved to the other location and put in the new directory structure where it was before. Your other option is to copy it to CD/DVD using the UDF format and do the same thing.
Hope this helps.