I figured it out!

Here's what I changed.

First of all, in the jinja2 template, I checked the email like this: {% if current_user.get_id() in artwork.votes %} instead of {% if artwork['votes'][current_user.get_id()] is defined%}.

Next, I changed the upvote function to be like this:

@app.route("/upvote", methods=["POST"])
def upvote():
    if current_user.is_authenticated:
        artwork = DisplayArtwork.objects(filename=request.form["filename"]).first()
        if artwork:
            user_email = current_user.get_id()
            if user_email in artwork.votes:
                artwork.update(pull__votes=user_email)
                return "downvoted", 200
            else:
                artwork.update(add_to_set__votes=user_email)
                return "upvoted", 200
        return "Failed to upvote", 500
    return "Login to upvote", 401

artwork.update(pull__votes=user_email) won't throw KeyError so I changed it to manually check whether the email was in the list and then decide what to do.

I also forgot to add .first() to get one artwork instead of a list.