it actually looks like perhaps Beyond Compare, one of my most essential tools -- may be able to do this flawlessly.. Another victory for BC... with the added bonus that I already own it!
I was going to suggest Beyond Compare, which I use for that purpose.
What was not clear from the original post was whether you want to keep the folder structure or copy files from multiple folders into a single folder.
I keep music organized in folders for each album within category folders, within overall type folders, so a specific track might be \Multimedia\MP3\Classical\Album_name\Track_number on my hard disk. I also keep a lot of identifying information in text, pdf and image files at various levels in that hierarchy, but don't want to copy most of that to the USB stick or SD card in a player.
BC preserves directory structure when copying and will copy only the files selected while creating the folder hierarchy containing them on the destination, starting from the base folders. So if I set \Multimedia\MP3\Classical\ as base on the hard disk and \Music\ on the USB stick, and copy \Multimedia\MP3\Classical\Album1\Track1 to the USB stick, the track will go to \Music\Album1\Track1, with folder Album1 created on the fly if it does not already exist in the destination base folder.
This is the way I do it, but if what you want is to place multiple selected tracks from different folders into a single folder on the destination end, you would use the "Copy to folder" command from the Action menu, then enter the destination folder and select "Don't keep folder structure" in the dialog box.
By the way, BC works great over ftp, so it can be used in much the same way to manage music and ebook collections over WiFi on Android devices that do not have removable SD cards (there are many Android ftp server apps on Google Play).