Actually I have had different experience. I had a Z visa, green book, and red book(foreign expert certificate), and when I left Beijing (aeroport), the only thing they checked was my visa. I did not show them the green book and my employer kept the red book. I still have my green book from last year, I took it out of the country. I never had any problems, they just checked the visa.

I returned this school year and applied for all new documents, NO PROBLEM!

All they check is the visa, they wont bother you unless you want them to! They are just aeroport customs officers, they are not the office of foreign affairs or Chinese Embassy, they don't know about all these little things like green books. They see hundreds of foreigners each day at the aeroport.
And, if you are afraid, or it is a big issue for you, then just take the train to Hong Kong, once you are in Hong Kong no one cares about all the PRC documents and visas. Then just leave through Hong Kong, no problems, no worries.