NO , As long as you renew your passport while in japan you wouldnt have any problems..
for that all you need is a jyuminhyou and a passport application
The biggest mistake for people to make is to register their green cards to Japanese embassy or apply for certain documents or try to get a new passport while outside of japan and thats how they ll get you. because a Japanese tourist can not renew a passport in a japanese embassy, if they lost their passport they can only get a passport card just to return to japan on a non-stop flight and not via another country .
so if you are a resident of u,s or another country you can show the resident card and you can get a new Japanese passport of documents you need
but if you become a u,s citizen and you try to get a new Japanese passport in a Japanese embassy than things may start going against you because they would report that you have a u,s nationality or another nationality to Japanese government and in that case MOJ would start coming after you ...
so if you dont want any questions you always renew your Japanese passport in japan
but you can renew your u,s or other passport either in japan or u,s and it would be ok,