I have a similar problem. I followed your steps above. In the ST3 folder the replaced file is shown with today’s date. When I refresh my song list in the app, and then sort the list from newest to oldest, the date displayed at the top of the list is several days ago — the last date I added a new song. Does the date indicate when the most recent song was added, but not its modified date?
The replaced song is just a slight tweak, so I can’t really tell by listening whether the song was actually replaced.
(Feature request: Perhaps the song info page could show when the file was first added, as well the date it was last modified.)