I had the same MAN-AMS-NRT itinerary last November.
The MAN-AMS leg was delayed, so I missed my connection in AMS. I went to the T4 transfer desk at AMS and they had automatically rerouted me on AMS-FRA-NRT, with the FRA-NRT leg on JAL.
I was in Business class, so it turned out to be a very nice flight from FRA.