Database
[{"_id":1,"obj":{"val1":1,"val3":3}},{"_id":2,"obj":{"val2":2,"val3":3}}]
Query
db.collection.update({"_id":{"$in":[1,2]}},[{"$set":{"obj.val1":{"$cond":[{"$ne":[{"$type":"$obj.val1"},"missing"]},12,"$$REMOVE"]},"obj.val2":{"$cond":[{"$ne":[{"$type":"$obj.val2"},"missing"]},22,"$$REMOVE"]},"obj.val3":{"$cond":[{"$ne":[{"$type":"$obj.val3"},"missing"]},32,"$$REMOVE"]}}}],{"multi":true})