Upstream has made no change to the tests since then.
I'd have expected upstream to fail as well, but it seems to not fail.

On latest upstream:
autoreconf -f -i
./configure
make -j
mkdir /var/empty
cd regress
$ PATH=`pwd`/..:$PATH:. TEST_SHELL=/bin/sh sh test-exec.sh `pwd` 
keygen-knownhosts.sh

Works !

I was able to track down further to a segfault in the bad case.
And in fact it seems to be related to a comment being in the hosts file:
Testable as easy as this:

 $ printf '#foo' > kh.test; ../ssh-keygen -qf ./kh.test -H

All else seem to be follow on issues.

I'll track down the segfault after lunch

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

Title:
  ssh-keygen -H corrupts already hashed entries

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