I can think of three options:
1) This is a no livestock village, and "sleep with the cows" is just an idiomatic expression. Little strange for such a village to exist in Medieval society, and strange for it to have such an expression when people could tell what village you came from by your speech.
2) The livestock disappeared just before or after the invitation to sleep there. Strange for the farmer to have used such an expression after his cows had vanished, and there was no bedlam like you might expect from disappearing livestock after Quentyn arrived.
3) Ralph goofed. But his goofs are ignorance (like putting a couple moons upside down...quickly corrected) or from writing WAY in advance of a storyline (I think this is how Ennias Longscript's "mistake" about Silver Spring/Freeman Downs came about...I may be wrong, of course). It would be weird of him to make such a blunder right in the story arc.