(4.6.2 -> 4.6.3 regression) Calling .set on a subfield of a deselected subdoc wipes out other fields on the subdoc

Suppose I have a schema defining a single embedded subdocument. I don't select this subdocument when I fetch the parent document, but I set a field on it anyway using .set.

In 4.6.2, this works as expected: the field I set changes, and the rest of the subdocument remains unchanged.

In 4.6.3, this wipes out the rest of the subdocument's fields, and gives it a new ID.

This feels like a bug, though it may be intended behavior.

``` javascript
const mongoose = require('mongoose');
const Promise = require('bluebird');

mongoose.Promise = Promise;
const connection = mongoose.connect('mongodb://localhost/minimal', {});
mongoose.set('debug', true);

const ballSchema = mongoose.Schema({
kind: String,
mass: Number
});

const sportSchema = mongoose.Schema({
ball: ballSchema
});

const Sport = mongoose.model('Sport', sportSchema);

new Sport({ball: {kind: 'birdie', mass: 4.75 }}).save()
.then((sport) => Sport.findById(sport._id).select('-ball'))
.then((sport) => {
sport.set('ball.kind', 'shuttlecock');

// On 4.6.2, this save issues this update:
// sports.update({ _id: ObjectId(...) },
// { '$set': { 'ball.kind': 'shuttlecock' } })
// On 4.6.3, it issues this update:
// sports.update({ _id: ObjectId("...") },
// { '$set': { ball: { kind: 'shuttlecock', _id: ObjectId("...") } } })
return sport.save();
})
.then((sport) => Sport.findById(sport._id).select('ball'))
.then((sport) => {
// On 4.6.2, sport.ball.mass === 4.7.5
// On 4.6.3, sport.ball.mass is undefined
console.log('sport.ball.mass', sport.ball.mass);
});
```

Start by running the supplied JavaScript reproduction against Mongoose 4.6.3 and compare the generated update with the 4.6.2 behavior. Trace the .set('ball.kind', ...) and subsequent save() path for a deselected subdocument. Done means changing kind preserves mass and the existing subdocument ID instead of replacing the whole subdocument.

Written by the indexing model from the issue text.