Japan is closed to entry, not to transit to foreign countries. People pass through to international targets from both HND and NRT daily (I just flew through both between LAX and BKK both ways). I also had a confirmed seat from HND to GMP in June, though I ended up canceling it due to having to move my trip out a couple weeks. Though that trip depended on GMP being open to international travel, otherwise yeah the flights end up canceled like they were for May.