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-You may talk to the local Chinese Police Department (派出所) to issue a name change certification/verification letter of your father (from Roman character to Pinyin), then do the notarization.

谢谢8老师。如果我父亲需要离开美国去处理这些手续。有什麽方法可以保留485并回到美国吗？还是只能放弃485。
-Then, your father may just write a statement to explain that his name was spelled in Roman character as "XXX" in his birth certificate based on the Chinese name spelling rule in Indonesia, and his name in his passport was spelled based on the Chinese name spelling rule in China as "YYY".

XXX means: your father's name in Roman; YYY means your father's name in Pinyin.