Database
[{id:"1234567890",answers:[{id:111,deleted:0},{id:222,deleted:0},{id:333,deleted:1},{id:444,deleted:1}]},{id:"0987654321",answers:[{id:111,deleted:0},{id:222,deleted:1},{id:333,deleted:1}]}]
Query
db.collection.aggregate([{$match:{id:"1234567890"}},{$addFields:{"answers":{$filter:{input:"$answers",as:"answer",cond:{$eq:["$$answer.deleted",1]}}}}}])