I had a similar problem on my FP3, as I could not delete several file entries from the Downloads folder using the default โFilesโ application, as I had deleted them using a different file manager. Therefore, even though they were not on the phone and I could not open them, it did show their name in the file list.
Well, by following these steps I have solved it, I can only see the files that I do have on my phone, so thank you very much!