Update after talking directly with AF over the phone:

1. Last First seat (1L) rebooked to honor my initial booking
2. JL046 was not an option as the F seat was a miles upgrade
3. Only other option would be CDG-AMS-ITM-HND (25h+ with a 10.5h transit in Osaka!) => no way

Among other points:

• Person on the phone was quite sure I wouldn't get compensated for the extra night in Paris (you can take the KLM flight via Osaka if you prefer to not spend another night in Paris)
• Didn't know if the private driver from hotel to CDG was still included with this booking.
• Was quite sure the increase in cost due the NRT instead of HND (after Covid quarantine you can't take taxi or public transportation, must arrange a private driver) would not be cover
• Was quite sure the difference in price (NRT return flight was cheaper than HND by about 1~1.5KEUR) would not be covered as well.

In any case, claims based on EC261 can only happen after the flight have been finished so I'll try to present my case after I return.

I'll try to negotiate miles instead of cash as a compensation, it's probably easier for them.

Thanks for your guidance and advice here!

Julien