As I recall, millipedes eat other insects, so no they are not harmful to the plants. Beneficial, in fact. Still, I'd refresh that soil before planting your new plants, adding at least half new potting soil to the mix. A healthy population of millipedes might mean there's somebody else living in there as well. Otherwise what have they been feeding on?
Or, you could dump those containers into your new raised bed, and start completely fresh.
