As I expected it also affects Debian (openssh-client 1:7.4p1-6)

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

Title:
  ssh-keygen -H corrupts already hashed entries

Status in openssh package in Ubuntu:
  Confirmed

Bug description:
  xenial @ 1:7.2p2-4ubuntu2.1 on amd64 has this bug. trusty @
  1:6.6p1-2ubuntu2.8 on amd64 does not have this bug. I have not tested
  any other ssh versions.

  The following should reproduce the issue:

  #ssh-keyscan XXXX > ~/.ssh/known_hosts
  # ssh root@XXXXX
  Permission denied (publickey).
  # ssh-keygen -H
  /root/.ssh/known_hosts updated.
  Original contents retained as /root/.ssh/known_hosts.old
  WARNING: /root/.ssh/known_hosts.old contains unhashed entries
  Delete this file to ensure privacy of hostnames
  # ssh root@XXXXXX
  Permission denied (publickey).
  # ssh-keygen -H
  /root/.ssh/known_hosts updated.
  Original contents retained as /root/.ssh/known_hosts.old
  WARNING: /root/.ssh/known_hosts.old contains unhashed entries
  Delete this file to ensure privacy of hostnames
  # ssh root@XXXXX
  The authenticity of host 'XXXXXX' can't be established.
  RSA key fingerprint is XXXXXX.
  Are you sure you want to continue connecting (yes/no)?

  # diff known_hosts.old known_hosts
  1c1
  < |1|BoAbRpUE3F5AzyprJcbjdepeDh8=|x/1AcaLxh45FlShmVQnlgx2qjxY= XXXXX
  ---
  > |1|nTPsoLxCugQyZi3pqOa2pc/cX64=|bUH5qwZlZPp8msMGHdLtslf3Huk= XXXXX

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