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Unspent Runes don't carry over. Neither do unspent whalebones, coins, or Bonecharms.
As such, you'll probably want to invest in the Bonecharm Crafting perk late in the game and upgrade it to Craft Runes. Then, before completing the game, you'll want to break down every Bonecharm you have and use your bounty of whalebones on crafting Runes. As mentioned above, you can't take it with you, so spend, spend, spend!
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