Thank you for taking the time to report this bug and helping to make
Ubuntu better. I appreciate the quality of this bug report and I'm sure
it'll be helpful to others experiencing the same issue.

As I proved in my checks this is an upstream bug. OTOH while annoying it
is not "very" fatal other than for convenience or certain automation
(which could code workarounds I think).

That said the best route to getting it fixed in Ubuntu in this case
would be to file an upstream bug. It would be great if you're able to do
that.

Otherwise, I'm not sure what we can do directly in Ubuntu to fix the
problem.

If you do end up filing an upstream bug, please link to it from here so we get 
auto-notified once there is something we can merge or even backport depending 
on the complexity.
Thanks!

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https://bugs.launchpad.net/bugs/1668093

Title:
  ssh-keygen -H corrupts already hashed entries

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