My little one is 2.5mo old and after her dad had to go away for the weekend and then got sick with…

My little one is 2.5mo old and after her dad had to go away for the weekend and then got sick with the flue, she cries when he tries to put to sleep at night. It's always been our routine but after those two incidents happen she acts like it's torture. I read that I should just leave the room or stay but not take over is just phase. She loves him during the day, feedings diaper changes, play time even naps except need time now no matter how tired she is. And last night I didn't take over it took about 20 min and she knocked out on him. I just feel so bad for him it was like their time and she loved it.