sample.xml

<?xml version="1.0" encoding="utf-8"?>
<ArrayOfBasicSetCollectionInfo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <BasicSetCollectionInfo>
    <SetName>Classic</SetName>
    <Cards>
      <CardInCollection>
        <AmountNonGolden>2</AmountNonGolden>
        <AmountGolden>0</AmountGolden>
        <CopiesInDecks>0</CopiesInDecks>
        <DesiredAmount>0</DesiredAmount>
        <CardId>CS1_069</CardId>
      </CardInCollection>
      <CardInCollection>
        <AmountNonGolden>2</AmountNonGolden>
        <AmountGolden>0</AmountGolden>
        <CopiesInDecks>0</CopiesInDecks>
        <DesiredAmount>1</DesiredAmount>
        <CardId>CS1_129</CardId>
      </CardInCollection>

sync.rb

require 'json'
require 'http'
require 'nokogiri'

DECKS = JSON.parse(HTTP.get('https://hsreplay.net/analytics/query/list_decks_by_win_rate/?GameType=RANKED_STANDARD&RankRange=LEGEND_THROUGH_TWENTY&TimeRange=CURRENT_EXPANSION'))['series']['data']
CARDS = JSON.parse(HTTP.get('https://api.hearthstonejson.com/v1/25770/enUS/cards.collectible.json'))

wanted_cards = {}

{ 219 => 'Odd Rogue',
  216 => 'Odd Paladin',
  134 => 'Zoo Warlock',
  179 => 'Spell Hunter',
  139 => 'Deathrattle Hunter',
  137 => 'Midrange Hunter',
  26  => 'Midrange Shaman',
  36  => 'Control Priest',
}.each do |archetype, deck_name|
  print deck_name
  DECKS.each do |_hero,decks|
    decks.
      sort_by{|d|d['total_games']}.reverse.
      select{|d| d['archetype_id'] == archetype}.
      first(8).
    each do |deck|
      print '.'
      JSON.parse(deck['deck_list']).each do |card_db_id, count|
        card_id = CARDS.detect{|card| card['dbfId'] == card_db_id}['id']
        wanted_cards[card_id] ||= 0
        wanted_cards[card_id] = [wanted_cards[card_id], count].max
      end
    end
  end
  puts
end

`cp Collection_Default.xml Collection_Default_#{Time.now.strftime('%Y%m%d%H%M%S')}.xml`

doc = File.open('Collection_Default.xml') { |f| Nokogiri::XML(f) }
builder = Nokogiri::XML::Builder.new(encoding: 'utf-8') do |xml|
  xml.ArrayOfBasicSetCollectionInfo('xmlns:xsi'=>"http://www.w3.org/2001/XMLSchema-instance", 'xmlns:xsd'=>"http://www.w3.org/2001/XMLSchema") do
    (doc/'BasicSetCollectionInfo').each do |set|
      xml.BasicSetCollectionInfo do
        xml.SetName (set/'SetName').text
        xml.Cards do
          (set/'CardInCollection').each do |card|
            xml.CardInCollection do
              xml.AmountNonGolden (card/'AmountNonGolden').text
              xml.AmountGolden    (card/'AmountGolden').text
              xml.CopiesInDecks   (card/'CopiesInDecks').text
              xml.DesiredAmount(wanted_cards[(card/'CardId').text] || 0)
              xml.CardId          (card/'CardId').text
            end
          end
        end
      end
    end
  end
end

File.open('Collection_Default.xml', 'w') do |f|
  f.puts builder.to_xml
end