[{_id:"1",transitions:[{"_id":"11","name":"Tr1","checkLists":[{_id:"111",name:"N1"},{_id:"112",name:"N2"}]},{"_id":"11","name":"Tr1","checkLists":[{_id:"1131",name:"N1"},{_id:"1312",name:"N2"}]}]}]

db.collection.aggregate([{$match:{"transitions.checkLists._id":"112"}},{"$addFields":{"transitions":{"$map":{"input":"$transitions","as":"t","in":{"$mergeObjects":["$$t",{"checkLists":{"$filter":{"input":"$$t.checkLists","as":"c","cond":{$eq:["$$c._id","112"]}}}}]}}}}},{"$addFields":{transitions:{$filter:{input:"$transitions",as:"elem",cond:{"$ne":["$$elem.checkLists",[]]}}}}}])