Visa to China for American living in Japan (no alien registration card)

My husband and I currently live in Japan, but will be moving back to the US at the end of our travel to China. We both had to get visa extensions, and the immigration officer extended the visa for 90 days, taking away our alien registration. In the process of applying for the Chinese visa, we were told that it would be automatically declined without the alien registration. Is there a way to complete the visa application? Would it be best to apply through the embassy in the US? We travel soon. Help!