Possibly because his existence had ceased to...well... Exist. Remember that even though both River and Amy are people that are "outside of the main time stream," and thus are usually not affected by this, Rory was part of both of their personal histories. Which means he could be erased from their memory, this should of course mean that River was erased as well. However because she is such a crazy time paradox it may be that she would have been one of the last things effected by the "Universe Erasing itself." Much like the Doctor.Because she knows she has not yet met him in his time line so acting familiar would confuse him greatly. She takes great care in also acting as if she doesnt know Amy when they first meet.

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