Question: Is there any way to download from Rio to PC and preserve the file names and directory structure that was used to upload to the Rio?

Jemplode allows you to re-create the playlist and/or soup structure when downloading. The files don't remember what they were like on the PC in the first place, so you can't make it go back to exactly what it was like on the PC. But you can get the PC's directory structure looking like the playlist structure on the player. Note that in Jemplode when you spec a filename specification, you can insert backslashes in the spec to force a directory (if I recall correctly), or you can use the option to create full pathnames at download.

Also, once you've got everything working again, have a look at this regarding keeping your player and your PC in perfect synch.

The download to my PC resulted in a flat directory with new filenames. It will be a pain to reconstruct the original directory structure.

If you want to post-process your files based on their tags, you can use MP3 Tag Studio, which can optionally re-organize the files into directories. However, your TAGS MUST BE FILLED OUT PROPERLY for this to work.

Did you make sure your tags were perfect before sending the songs to the player? If they were, you should be OK. If they were not, you need to click here and read it carefully.