You receive a message that the partition cannot be deleted because it is not empty, even though there are 0 leads in the partition.
Marketo will give you this error message when you have a partition with anonymous leads in it. Even if you move all known leads from a partition, there will still be hidden anonymous leads. This will prevent you from deleting the partition. Contact Marketo Support to have the anonymous leads removed from the partition so that you can delete it.