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I'd like to have a single method that either creates or updates a document for a policy. Searching and trying different techniques like this one, I have come up with a null _id for my document. Using findByIdAndUpdate has a similar affect.

I see a document inserted in the collection, but the _id field is null:

exports.savePolicy = function (plcy, callback) {
    console.log('priority is : ' + plcy.priority)
    try {
        var policy = new Policy(plcy);
        var query = {_id: plcy._id};  //this may be null
        var update = {
            name: plcy.name || defaults.policyDefaults.name,
            longDescription: plcy.longDescription || defaults.policyDefaults.longDescription,
            shortDescription: plcy.shortDescription || defaults.policyDefaults.shortDescription,
            priority: plcy.priority, colorHex: plcy.colorHex || defaults.policyDefaults.colorHex,
            settings: plcy.settings || [],
            parentPolicyId: plcy.parentPolicyId || null
        }

        Policy.findOneAndUpdate(query, update, {upsert: true}, function (err, data) {
            callback(err, data);
        });

    } catch (e) {
        log.error('Exception while trying to save policy: ' + e.message);
        callback(e, null);
    }

Is there something that can be done to get the _id not to be null when its not an update?

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null is a valid _id value in MongoDB, so if you don't want it used in new docs you must ensure that a null value is replaced with a new ObjectID in query:

var query = {_id: plcy._id};
if (!query._id) {
    query._id = new mongoose.mongo.ObjectID();
}

// the rest stays the same...

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