Texture paths are set in the md3. If you want to change it you'll have to edit the md3 too.
The _remap key can help too.
"_remap" "models/mapobjects/coolthing/cooltexture;models/mapobjects/ingar/othertexture"
This will replace the texture coolthing/cooltexture in the model with ingar/othertexture
You can use it to replace a single texture or an entire directory.
Replacing multiple textures from multiple directories won't work.