Following command edits the bare repo (rather than a clone of the repo)
cd bare_git_repo
git filter-branch --prune-empty -d /Users/username/software/git_test/git_backup --index-filter "git rm --cached -f --ignore-unmatch a_large_binary" --tag-name-filter cat -- --all
Then run the following on the bare repo
git update-ref -d refs/original/refs/heads/master
git reflog expire --expire=now --all
git gc --prune=now