Remove a whole 3rd level json array using query

There is no array inside id 28000007. You need to post full document and expecting output.
Otherwise it is very difficult.

{
  "id": 0,
  "avatar": {
    "name": "blabla",
	"hero_upgrade": [
      {
        "id": 28000007,
        "list": [1,2,3,4]
        "cnt": 29
      },
      {
        "id": 28000002,
        "cnt": 49
      }
    ]
  },
  "jsonType": "data"
}

If you want remove list where id 28000007

UPDATE `magic-players`
UNSET  hu.list  FOR hu IN avatar.hero_upgrade  WHEN v.id == 28000007 END
WHERE jsonType = "data" AND
ANY v IN avatar.hero_upgrade SATISFIES v.id = 28000007 AND v.list IS NOT MISSING END;

Check Examples 3-5 https://docs.couchbase.com/server/current/n1ql/n1ql-language-reference/update.html