FDISK does not see NTFS logical drives in an extended partition, and simply ignores their presence.

If you have a primary FAT partition (C:), and configure 2 logical drives in an extended partition, NTFS (D:) and FAT (E:), running FDISK will dispay C: and D:, but D: will really be the E: FAT partition. If you delete D:, you will really be deleting the FAT partition on E:

Always use Disk Administrator (WINDISK.EXE) to make changes to logical drives in a mixed FAT / NTFS environment.