Day effect: "Place the Day/Night Card on its night side. When resolving one card in the castle keep stack with the apple modifier, ignore its effect(s) and -1 to any one stat instead. Then, flip the Day/Night Card."
You only resolve the apple effect once -- it can only be triggered on one apple in the whole stack, not each apple. The “Then flip” text is tied to the apple modifier text, so after you ignore the apple effect and reduce a stat, you flip the Day/Night card.
Night effect: "At the start of the next Engagement that takes place at night while the Evil Stepmother is active, select a random castle card from the box. The Evil Stepmother gains its night effect and +1 damage."
The nighttime effect only happens once, the “next” engagement. But the nighttime effect she steals from whatever card is taken from the box, is a nighttime effect she retains for the rest of the game, and is “on” whenever the engagement starts at night. The +1 damage she gains also is only “on” when it’s night. So you’re incentivized to get it flipped back to day (perhaps, with the apple ability above).