swapon -a by default only enables swap partitions that are in fstab, and
ecryptfs-setup-swap comments the old swap's line there, so the correct
swap is mounted on boot. And with the encrypted swap as provided by
ecryptfs-setup-swap, hibernate is not possible so you shouldn't mind
overwriting data from a previous session.

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https://bugs.launchpad.net/bugs/953875

Title:
  Encrypted swap no longer mounted at bootup

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