db={collectionA:[{_id:ObjectId("5a934e000102030405000000"),some_ids_of_b:["id1","id3"]}],collectionB:[{_id:"id1"},{_id:"id2"},{_id:"id3"},{_id:"id4"}]}

db.collectionB.aggregate([{$lookup:{from:"collectionA",let:{my_id:"$_id"},pipeline:[{$match:{$and:[{_id:ObjectId("5a934e000102030405000000")},{$expr:{$in:["$$my_id","$some_ids_of_b"]}}]}},{$project:{_id:1}}],as:"some_ids_of_b"}},{$match:{"some_ids_of_b.0":{$exists:false}}},{$unset:"some_ids_of_b"}])