Thank you Joe!
That was the solution! (suggestion: would be nice if the old repo could have a deprecation message with instructions to upgrade to new one).
For other readers, here is what I did to upgrade the Virtualmin GPL installs to new repo:
curl -L https://software.virtualmin.com/lib/RPM-GPG-KEY-virtualmin-6 | apt-key add -
vi /etc/apt/sources.list
and replace:
deb http://software.virtualmin.com/gpl/ubuntu/ virtualmin-xenial main
deb http://software.virtualmin.com/gpl/ubuntu/ virtualmin-universal main
by:
deb http://software.virtualmin.com/vm/6/gpl/apt virtualmin-xenial main
deb http://software.virtualmin.com/vm/6/gpl/apt virtualmin-universal main