Thanks for the bug report Evgeny and for the initial investigation,
Lena.

The following commit "fixes" the issue:

commit f2d84f1b3fa68d77c99238d4c645d0266fae2a74
Author:     d...@openbsd.org <d...@openbsd.org>
AuthorDate: Wed May 13 09:55:57 2020 +0000
Commit:     Damien Miller <d...@mindrot.org>
CommitDate: Wed May 27 10:09:19 2020 +1000

I say "fixes" because it doesn't do exactly what Evgeny is asking in the
bug description; that is, it doesn't make ssh-keygen preserve *all* of
the permission bits.  Instead, with the commit above applied we see that
ssh-keygen in Focal/Bionic start behaving exactly like what we see in
Impish/Jammy, and the group/all *read* permissions are preserved, but
not the (e.g.) execute permission.  We can see that on the output that
Lena pasted.

Either way, preserving the "read" permission bits for group/all and
dropping everything else is done on purpose, as can be seen on this
excerpt (from ssh-keygen.c:do_known_hosts):

...
    fchmod(fd, sb.st_mode & 0644);
...


I have already backported & tested the patch on Bionic, and it works.  I will 
start filing MPs tomorrow.

** Changed in: openssh (Ubuntu Bionic)
     Assignee: (unassigned) => Sergio Durigan Junior (sergiodj)

** Changed in: openssh (Ubuntu Focal)
     Assignee: (unassigned) => Sergio Durigan Junior (sergiodj)

** Changed in: openssh (Ubuntu Bionic)
       Status: Confirmed => Triaged

** Changed in: openssh (Ubuntu Bionic)
       Status: Triaged => In Progress

** Changed in: openssh (Ubuntu Focal)
       Status: Confirmed => In Progress

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https://bugs.launchpad.net/bugs/1966591

Title:
  ssh-keygen -R changes known_hosts file permissions (mode)

Status in portable OpenSSH:
  Unknown
Status in openssh package in Ubuntu:
  Fix Released
Status in openssh source package in Bionic:
  In Progress
Status in openssh source package in Focal:
  In Progress
Status in openssh source package in Impish:
  Fix Released
Status in openssh source package in Jammy:
  Fix Released

Bug description:
  When I use ssh-keygen -R to remove a host from known_hosts it changes
  permissions on the file. This causes problems particularly when used
  on the global known hosts file (/etc/ssh/ssh_known_hosts), because
  then only root can read it. Programs running non-interactively as non-
  root users suddenly fail to SSH and it's not immediately obvious why.

  To reproduce:

  $ ssh-keyscan github.com >test_known_hosts
  $ chmod 741 test_known_hosts
  $ ssh-keygen -R github.com -f test_known_hosts
  $ stat test_known_hosts
  ...
  Access: (0600/-rw-------) ...

  Expected behavior: file permissions remain unchanged (mode 0741 in
  this example).

  $ lsb_release -rd
  Description:  Ubuntu 18.04.6 LTS
  Release:      18.04

  $ apt-cache policy openssh-client
  openssh-client:
    Installed: 1:7.6p1-4ubuntu0.6

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