The odds are pretty good the old one is still around somewhere in your project.
Once trick that I've used before to find out if something is still in the project somewhere is to open the project file with a text editor. (BareBones Softeware's BBEdit is great, but their freeware Text Wrangler will also work just fine for this.)
Once it is open just search for the "bad" file and search the entire project. You might find it there and that will help you track it down. You can edit this file but be careful, it is XML and it had better still be valid XML when you save it.