-It suddenly being called Geass in R2 WAS crappy writing. During the R1 project they went to extra lengths to point that out in the side materials. Aside from the Mao deal mentioned earlier, C.C. herself at the start had no clue WTF lelouch was talking about when he said Geass. Also in the DS came, Castor and Pollux call it their own thing as well. "the blessed".
-Shirley never remembered on her own. She simply knew the info from the letter, but didn't know what to make of it until LOYALTY broke the geass. And Chalulu can't erase memories, only manipulate them. But if a person forgets a memory on their own, it's lost. Such as Lelouch's memories of Anya. He simply forgo about her over those 8 years.
So along with that, they erased the memories of her remembering that Lelouch was Zero. (As shown when she gets her memories back in Turn 12.Of course, this is her knowing it from the first time she lost her memories.)
Charles nor V.V. knew anything about her knowing Lelouch was Zero. The only thing Charles did was alter the Nunnaly memories. The memory of LuRo was already Geassed away from lelouch himself. Orange just broke both geasses at the same time.