Some thoughts:
1. Regarding losing files because of overwriting files with the same name: I just tried to make this happen on purpose. I renamed a file to the name of a file that was already in the directory. I was hoping for a warning message, or a failure. Instead it just silently did the rename. HOWEVER, it added a "1" to the new file name. So the old file that I was going to overwrite remained intact. The file that I changed attempting to cause a problem, was renamed with the "1" in it. So both files were preserved. This is good. It's bad that it might be hard to locate these in the future, but you can be pretty confident that the Rename, Move, and Copy tool won't lose any files due to over writing them.
2. As another poster said, having your metadata filled out will really help make your file structure organized. As long as each song has unique information that you *use* in the file and directory names, you should end up with pretty much exactly what you want.
3. You can test some of this yourself without doing any moves. You mention a lot of reissued or remastered albums. Go find a few of them in your library. Do the albums have unique names? For example, Dark Side Of The Moon, versus Dark Side Of The Moon (Mobile Fidelity). If you find any albums with the *exact* same name and exact same artist, you'd have to figure out some way to distinguish them. Frankly, I wouldn't want to have that condition in my library to start with. It would make figuring out which album I wanted much more difficult.
As long as you have a unique combination of Artist and Album for each album in question, I think you're good to go.
4. You might try moving a small portion of your library to start. Maybe one album. Then if that works, try several albums. Maybe intentionally pick two different versions of the same album, in order to test the uniqueness of the file names it will come up with. The good news here is that the Rename, Move, and Copy tool has a preview pane over on the right. So before you ever press OK, you can see exactly how it is going to rename your files. You will probably need to hover over entries in that pane, as they tend to be so big that they won't display in the window. But hovering over them will bring up a pop up box to show you the full file name and path before and after. Give it a try!
5. If it was me doing this, I think I'd pick a new root folder to put all of my music in. Something that makes sense as the *one* place where it will all be. Then I'd start doing these renames and moves into that parent folder. Of course with child folders underneath with Artist, Album, etc directories. As you go along, the original folders will get emptied out. Eventually, the original folders will all be empty and all of your music will be in one folder structure. It might be easier than you think, as long as your early experiments go well. If you are confident after the first 4, 5, 6 trial runs that it's going to work, you can select everything and just let it run until it's done.
6. Be careful and certainly have backups, as has already been WISELY mentioned.
Good luck!
Brian.
