I use mp3tag to create subset of files from my mp3's (after filters etc) and then drag-n-drop them into my SD card for playback in my handheld (Treo 650). My mp3's are in different directories on my PC, the directory tree being arranged by Genre-artist-album.
This works because mp3tag copies the files when I drag-n-drop them to my SD card (in a card reader), the source and destination being on different storage volumes.
I tried a different way, by copying the files to a subdirectory (called Transfer) on the hard drive (i did not have my SD card handy at that time) for copying to my card at a later time. Unfortunately, the Transfer directory was on the same storage volume as my mp3 collection. The drag-n-drop ended up MOVING the files to this directory, destroying the careful directory structure.
Could it be a global option in the future to always make drag-n-drop a Copy or a Move (user selectable)? Or to pop-up a confirmation dialog, especially for Move operation (which results in eventual deletion of the source files) : "Do you really want to MOVE the files?"