Sometimes when working offline, I merge branches, and then I delete the old (merged) branches. 
It is best to do so online, as you can follow up with a push --delete, as in this answer:
git branch -r --merged | grep -v master | sed 's/origin\///' | xargs -n 1 git push --delete origin
But since you deleted your branch locally (offline), you need, when online, to fetch --prune the remote branches from GitHub, check if their local counterpart does exist, and push --delete otherwise.
Use git for-each-ref with the refname:lstrip=3 format in order to list the short names of those remote branches:
 git for-each-ref --format='%(refname:lstrip=3)' refs/remotes/origin
You can check if a local branch does exists with git show-ref --quiet
if git show-ref --quiet refs/heads/develop; then
    echo develop branch exists
fi
So you can easily combine the two.
git fetch --prune
for branch in $(git for-each-ref --format='%(refname:lstrip=3)' refs/remotes/origin); do
    if ! git show-ref --quiet refs/heads/${branch}; then
        echo "delete remote branch '${branch}'"
        git push origin --delete ${branch} 
    fi
done