Our guineas started acting more scared of us after a predation incident. They still want to go in the pen at night (usually, but there were a few days when dinner was not enticing), but they do yell at us more often. We've been herding them- we just walk behind them or out to the side- to get them to walk toward the pen we've set up. Something I'm trying is to add a few treats (like meal worms) to the feed they get in the evening in hopes this will increase their motivation to shift back into their pen in the evening.
Also, we kept ours penned for 8 weeks straight before letting them roam at all. They may need to re-learn where "home" is. Now, even if they aren't interested in the dinner we offer, they'll still wander back in and we can close them up for the night.
Good luck!