I think my preference would be to preserve all settings, Highlighting all tracks in your collection (in Rekordbox 6) and deleting will just remove the track associations and leave all your settings intact. These changes should not affect Rekordbox 5, but I have never tried it.
As far as the settings go, you can set some to default, but I think they have to be done separately within the program.
I would definitely backup the database and your music files before doing anything. Just in case something goes wrong or you change your mind later.
Keep in mind that you are starting with a fresh library. Any songs you associate with it will not have any hot cues or memory cues and will need to be re-analyzed.
@Pulse may have something to add to this.