Several folks have asked about passport renewals. If you renew your passport, you must re-apply for the program all over again. The physical card is tied to your passport number and cannot be changed. If you renew your passport, you will have a new passport number, so you need to apply for a new card. I verified that this is the process several times via e-mail and phone calls with them (had a local person do this on my behalf due to the language barrier).
To submit a new application for the new passport, log into the TTP website, and select the "Enter application information" button to start the process.
I renewed my passport back in March, and immediately re-applied for the TTP program. It took about 70 days from the time I submitted the application to the Secondary Inspection phase. Had to go back to HND, submit the same paperwork all over again with the revenue stamp fee, and then I ended up with a new card. I still have the old card (at no point do you need to surrender the old card since this is a brand new application).
Someone earlier in the thread asked about using the QR code in the old passport plus the TTP card to try and enter Japan after renewing a passport. Probably not a good idea as you would be attempting to enter the country on an invalid passport number. FYI - they did not put a QR code in my new passport (are they still doing that?)