Short answer: It will not overwrite them. They are completely separate sound files.
Long answer: If an old file on your LM has exactly the same file name as the new file, and I do mean exactly, down to the last letter it will be overwritten. If the old file is not named exactly the same as the new file you'll end up with both the old file and the new file stored on the LM (assuming there is enough free memory on the LM for both the old and new files to be stored on the LM at the same time).
Since your talking prime mover sounds if you have the EMD 645 Turbo on the LM and you want the EMD 645 Turbo ULT the old one will not be overwritten, you'll have to delete the old one yourself.
You can delete the old sound file before copying the new sound file or you can delete the old one after copying the new file It doesn't particularly matter which way around you do it.
- Tim