Another possibility. This episode is the death of The Jolly Roger. We find out what happened to it within the one year time span.
Perhaps Hook had to sell it or get rid of it in order to go and get Emma. Maybe this was one of his sacrifices to get to her that he had to make?
I just remembered what Hook said in Tiny, the Jolly Roger is made from the same enchanted wood as Emma’s wardrobe. So this could have been the only solution that Hook could use in order to get to her, sacrifice the jolly.
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