I'm no expert, but perhaps the files have uncommon characters in the filenames. I've downloaded some songs from artists on youtube that have japanese characters or other special characters, and Spotify couldn't recognize the names. As far as I've noticed, it hasn't changed the files at all; just the names were different.
I have my files stored in Google Drive and Spotify just reads them from a file shortcut on my desktop, if that changes anything. If you're worried about the data being corrupted you could make a backup copy.