If you are modifyed some file automaticaly like log , cache in any application , web site on development or live . you does`t  want to update that particular file into your git repository .

You have a question about How to change Git updated index to previous index setting , just use this following comment in your comment line with current available git copy of your folder .

find {your folder} -type f -exec git update-index --assume-unchanged '{}' \;

for example from magento change the index of media folder

find media/catalog/product/v/ -type f -exec git update-index --assume-unchanged '{}' \;