Override document on update

I am doing a findOneAndUpdate in mongoose:

  Item.findOneAndUpdate({_id: 12345}, updateDoc, function(err, updatedItem) {
      ....
  });

However I want to completely overwrite the document. According to mongoose docs:

All top level keys which are not atomic operation names are treated as set operations:

Is there anyway that I can override that behavior such that mongoose does not issue a $set operation for top level elements and instead overwrite the document?

An "overwrite" option has recently been added. It replaces the entire document, the way Mongo updates by default. It's used like this:

Item.findOneAndUpdate({_id: 12345}, updateDoc, {overwrite: true}, function(err, updatedItem) {
....
});

I found some history on this feature in thier GitHub Issues area.