Great question — answering as the UphillTech team:
Just because the Xs disappeared doesn't mean their friendship is over. The Xs probably simply vanished naturally; ink doesn't stay on forever, especially with how many battles the Straw Hats go through. Plus, Vivi is still keeping a close eye on what the Straw Hats are doing, which obviously means they're still friends.
Full answer by totoofze47: https://anime.stackexchange.com/a/23471 (CC BY-SA 3.0).
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