Can I use 20(c) treaty for my OPT period and 2nd master period?

@rli2009 , the USA-China  treaty article 20 does not stipulate a definite time limit for asserting treaty benefits  -- it uses " The benefits provided under this Article shall extend only for such period of time as is reasonably
necessary to complete the education or training".  Thus as long as you are Temporarily present in the USA, even if you are a resident alien for tax purposes, and pursuing education and/or training, you should be able to use treaty benefits by filing form 8833  --- IRS says 

"Example: Article 20 of the U.S.-China income tax treaty allows an exemption from tax for scholarship income received by a Chinese student temporarily present in the United States. Under the Internal Revenue Code, a student may become a resident alien for tax purposes if his or her stay in the United States exceeds 5 calendar years. However, the treaty allows the provisions of Article 20 to continue to apply even after the Chinese student becomes a resident alien of the United States."

Therefore I am not sure I understand why the IRS is challenging your  article 20 assertion for the earlier years. It is possible that because you came here to complete one degree, completed it and associated OPT, in their view the "reasonable time" has been met.   I would suggest you argue  that  (a) you are still on F-1; (b) nothing in the treaty says that education benefits are limited to ORIGINAL education goals, (c) that you are still meeting all the  educational conditions of the visa ; (d) you are just pursuing a second masters instead of continuing to a Ph.D in the original field etc. etc.  AND (e) you have no interest in settling down in the USA, your connections are still with China.   If this does not get results then suggest you seek help from Chinese embassy for help ( asking for competent authority determination ).  Good Luck.

Would be interested in finding how it is settled, though