The unignore file is for getting the database to take notice of a sub-directory of something you've marked as wanting the database to ignore.
For Example, lets say you have the following folders on your DAP :
Music/Random Files/Podcasts
You have a database.ignore file in your "Random Files" directory - but you'd like the database to index the content of "Podcasts".
With the old behaviour, you'd need to move the "Podcasts" directory outside of "Random Files", since the database.ignore file in it would exclude everything in it, including the subdirectory "Podcasts". Now though, you can an a database.unignore file into "Podcasts", and the database will add it's content on the next scan.