As Poppet Factory transforms back into Poppet Stitcher, the effect making your creature tokens 3/3 and making them lose their abilities ends. Their base powers and toughnesses will revert to whatever they were before that effect started applying, although other effects that modify power and/or toughness, such as ones created by Auras, counters, and the like may still apply. They'll also have whatever abilities they had before they lost them.