Son Born in China Holding Malaysia Passport - Leaving for Malaysia & Returning to China

Hi...
My son is born in China and had obtained a Malaysia passport via one of the General Consulate in China. His mother is a Chinese holding China passport and me being a Malaysian working in China.

We planned to go back to Malaysia for a short visit. Had obtained an Exit & Entry Permit for my son to leave China.

Now the question is how to bring him back to China after our short visit. Can I apply for a Single Entry China Tourist Visa for him to enter China and change to a Resident Visa at the local Entry / Exit Immigration Bureau where his mother "hukou" is located.

At the Inquiry Desk of China Entry / Exit Immigration Bureau said that my son's Malaysia passport Place of Birth is China, so the overseas China Embassy might not issue any visa for him and he has to use the Exit & Entry Permit to re-enter China which is only valid for one exit & entry.

We are confused and lost. Any guidance would be much appreciated as I am sure we are not the first family to encounter this issue.