FDISK is not completely compatible with NTFS partitions, which causes it to mess up when deleting non-primary NTFS partitions.

Cannot delete Extended DOS Partition while logical drives exist

No Logical Drives defined

To make up for that Microsoft created the utility Delpart.exe (Download Mirror), which makes it possible to delete logical NTFS partitions within an extended partition without deleting the wrong partitions.

More info MS KB261473
More info MS KB310359