"This more seems like a transitional period," the source says.
The two even celebrated the holidays with their three children: Violet, 10, Seraphina, 6, and Samuel, 3, in the mountains of Montana.
According to the source, the actor continues to stay in the guest house on the family's L.A. property as he and Garner remain focused on parenting.
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"They interact every day. Mostly about the kids and simple things," the source adds. "Jen wants Ben around for the kids."
After the New Year, Affleck, 43, will continue to shoot his new period film, Live By Night, on which he serves as screenwriter, director and actor. Meanwhile, Garner, 43, will begin promoting her new film, Miracles From Heaven.
"Jen's doing great now," says the source. "It's hard to imagine her changing her mind."