I contacted them on FB about flights I took on the 31st that credited according to the new system. They said they'd look into it, then came back again today with the following
"We are currently working on the launch of the reinvented Flying Blue programme. For now almost all Flying Blue systems are up and running again but at the moment we are not able to claim any missing Miles. From the moment this is possible again, we will handle your request."
Interesting to see what happens.