How to delete a node

You should try something like this

upsert {
  query {
    v as var(func: uid(0x24a1a)){
     incoming as <~User.api_key_sets>
     }
  }

  mutation {
    delete {
      uid(v) * * .
      uid(incoming) <User.api_key_sets> uid(v) .
    }
  }
}