var pipeline = [
  {$lookup:{
      from: "files",
      localField: "files_id",
      foreignField: "_id",
      as: "file"
    }
  },
  {$match:{
      "file.uploadDate":
      {
        $lt: ISODate("2017-06-10T00:00:00.000Z")
      }
    }
  }
];

var cursor = db.chunks.aggregate(pipeline);
var chunkIds = cursor.map(function (chunk) { return chunk._id; });
db.chunks.remove({"_id": { "$in": chunkIds }});