IT WORKS !
Excellent
So the smoking gun is: * Never point the primary Domain to an i-bay directory * it had worked for me in the past, but not since the update...
Hmmm. I'm not sure exactly what you did, but clearly it messed things up. If this is the case then you really should open a bug for it because the issue is still there.
Note...
I believe for /.well-known/acme-challenge/ every domain is actually pointed to the Primary ibay - check /etc/httpd/conf.httpd.conf regardless of anything else.
e.g.
<VirtualHost 0.0.0.0:80>
Servername host.domain.com
... blah
Alias /.well-known/acme-challenge/ /home/e-smith/files/ibays/Primary/html/.well-known/acme-challenge/
</VirtualHost>
It is too difficult to try and make letsencrypt/dehydrated add keys to lots of different directories so they all have to go in one place.
Im happy to resolved by my self
Indeed. Next time have a good think of what you might have done to upset things yourself before jumping up and down and saying 'urgent'
Sometimes things that you modify might take a few days for say a reconfigure/reboot to show themselves. So you really ought to check logs etc to see what you might have changed before jumping to conclusions.
However, it is only part resolved (worked before, doesn't work now unless you revert your modification) and you really ought to create a bug.