Yes, those agents was just stupid.
I had the same case -- upgraded P fare by cash FRA-EZE to First and ticket was reissued with new booking class A. And I got 3xstatus/HON miles for that segment (actually 3,25x as the execuitve bonus alos applied).
Some information is here (altough not very clear):
https://www.lufthansa.com/am/en/upgrade-first-class
Actually if LH.com is offering you upgrade, I think even there are mentioned more miles.