> db.test.remove()
> db.test.update({ "name" : "first" , "pic" : { "$ref" : "Pic", "$id" : ObjectId("4c48d04cd33a5a92628c9af6") }}, {$set:{}}, true, true)
> db.test.find()

{ "_id" : ObjectId("4c48d2c9280e000000004377"), "name" : "first" }

The pic field is not saved; The actual update is more complicated but this is reduced to the minimum.

This was originally a problem from the 2.0 java driver but I doubt that has any bearing on the server.