Posting here after a long time. I am afraid, I would not be able to help you in terms of G.O. but I can refer to a case that has happened to a colleague of mine.
The said colleague joined service as an Assistant teacher in the Pass category on November 2002. After having completed his B.Ed in 2008, he appeared for SSC and got appointed to another school in the PG category in 2009. His percentage in MA was about 45% only. Later on he got admitted to Chhatrapati Shahuji Maharaj University, Kanpur and secured well over 55%. He has used that degree and appeared for NET and qualified as well. However, he is still working in the same school.
For his school, his older PG degree still holds good as that is the one that he has used to get the job in the first place. However, he has the same degree in the same subject from another university. This is a confusing situation. I have no idea of the legal implications of this situations.