Hm, what did you change in them? Not the file names, obviously, or else they wouldn't have overwritten the old ones. But yeah, they were the 3 files in the "misc" directory, I believe.
OK, as an example torture_frame.nif:
Originally (as reported by NifTexture):
\Data Files\Textures/TX_C_slavebracers.bmp
\Data Files\Textures\Tx_metal_iron_rusty_01.tga
\Data Files\Textures\Tx_metal_iron_rusty_strip_01.tga
\..\Textures\Tx_metal_manacle_01.tga
\..\Textures\Tx_metal_manacle_02.tga
\Data Files\Textures\Tx_metal_strip_01.tga
\Data Files\Textures\Tx_velothi_doorstrip_01.tga
Changed to:
TX_C_slavebracers.bmp
Tx_metal_iron_rusty_01.tga
Tx_metal_iron_rusty_strip_01.tga
Tx_metal_manacle_01.tga
Tx_metal_manacle_02.tga
Tx_metal_strip_01.tga
Tx_velothi_doorstrip_01.tga
The three files I changed in a similar way:
PillarManacles.nif
skell2.nif
torture_frame.nif