Database
[{"variants":[{"fruits":[{"bad_name":"Banana"}]}]}]
Query
db.collection.update({},[{$set:{variants:{$map:{input:"$variants",as:"v",in:{$mergeObjects:["$$v",{fruits:{$map:{input:"$$v.fruits",in:{$mergeObjects:["$$this",{good_name:"$$this.bad_name"}]}}}}]}}}}},{$unset:"variants.fruits.bad_name"}])