I am constantly amazed at how many people believe the only way to change the storage option of a hard drive from FAT or FAT32 to NTFS is by means of formatting the hard drive.
the following command line (DOS) should eliminate all those issues (execute (command shell) on any drive other than the drive being changed):
CONVERT <volume> /FS:NTFS [/V] [/CvtArea:filename] [/NoSecurity] [/X]
volume Specifies the drive letter (followed by a colon), mount point, or volume name.
/FS:NTFS Specifies that the volume will be converted to NTFS.
/V Specifies that Convert will be run in verbose mode.
/CvtArea:filename Specifies a contiguous file in the root directory
that will be the place holder for NTFS system files.
/NoSecurity Specifies that the security settings on the converted
files and directories allow access by all users.
/X Forces the volume to dismount first if necessary. All open handles to the volume will not be valid.