Database
[{"_id":"a74e283a","data":[{"origin":"apple","edit":"fruit"},{"origin":"grape","edit":"fruit"},{"origin":"melon","edit":"fruit"}]}]
Query
db.collection.update({},[{"$set":{"data":{"$let":{"vars":{"ndata":[{"origin":"apple","edit":"fruit_edit"},{"origin":"pear","edit":"fruit"}]},"in":{"$let":{"vars":{"ndata_origin":"$$ndata.origin"},"in":{"$concatArrays":[{"$filter":{"input":"$data","cond":{"$not":[{"$in":["$$this.origin","$$ndata_origin"]}]}}},"$$ndata"]}}}}}}}])