OP
Are you transferring International to International or to a Domestic flight?

If it's to a Domestic you need to actually enter Japan at Haneda (Health, Immigration, Customs).

If you're going International then as TBS says you'll need some help getting out. Usually the Lounge staff can help but you'll need to make sure that you've got all of your QR codes (or Blue Quarantine screen) ready since you'll need to arrive and depart Japan. They can also make sure that you've got the right boarding pass so you can just head straight to Security and Immigration on the way back in and bypass the check in desk.