I'm guessing that the HD you want to remove is connected via USB, and I'm just guessing at the software you're using to access the device.
Here's my experience, none of which has messed up the NTFS partition on a USB mounted drive:
- type "sync" in a terminal before removing drive (this flushes from the IO cache to the disk). Is it necessary? I dunno.
- thunar has an "Eject" option. It'll incorrectly say that it's still writing data...ignore it.
- pcmanfm has "unmount" but no "eject" - it'll usually crash when it "unmounts" the partition.
IOW, thunar and pcmanfm are buggy and therefore suck, but they don't break the NTFS partition or drive.