Database

[{_id:"12312",notifications:[{_id:"1",status:"unread"},{_id:"2",status:"unread"},{_id:"3",status:"unread"}]}]

Query

db.collection.update({"_id":"12312"},[{"$set":{"notifications":{"$map":{"input":"$notifications","as":"n","in":{"$cond":{"if":{"$in":["$$n._id",["1","2"]]},"then":{"$mergeObjects":["$$n",{"status":"read"}]},"else":"$$n"}}}}}}],{multi:true})

Result