Try turning it off;
sudo mdutil -i off /Volumes/your_hard_drive_name_1
Then remove the indexes;
sudo mdutil -E /Volumes/your_hard_drive_name_1
Physically remove the .Spotlight directories from the root of each drive.
$ cd /
$ sudo rm -fr .Spotlight-V100
Use mdutil again to turn indexing back on for each drive
$ sudo mdutil -i on /Volumes/your_hard_drive_name_1