Delete Duplicates works best when you have MusicBrainz Ids rather than just finding duplicates based on textual metadata such as artist and title, but you will not have this until you run Fix Songs first.
So you should always run Fix Songs first, and then run Delete Duplicates afterwards (and use a suitable choice for matching). The main feature of SongKong is song identification, and without accurately identifying songs its not possible to accurately find duplicate songs.
When you run Delete Duplicates ensure that you have set Song is a duplicate if has same to a suitable MusicBrainz based option such as Song is a Duplicate Filename to Same MusicBrainz song and album (specific version)
