Make Git “LF will be replaced by CRLF” warnings go away

This might happen if you change core.autocrlf config variable (if I understand your problem correctly).

If you are at clean state, i.e. just after commit, and you don’t have uncomitted changes, forced re-checkout and removing index should do the trick:

The below command git reset --hard HEAD will make your current branch to point to the latest commit and all uncommitted code will be lost. Make sure to commit the code or take the backup

$ rm .git/index
$ git reset --hard HEAD

That, I think, would sync both working area files, and the index (staging area) to follow crlf settings.