Emma not telling Flap she also cheated
It's interesting, my first reaction in that scene when Flap feels guilty about cheating on Emma, was something like "OK, Debra Winger you also cheated, tell Jeff Daniels that he shouldn't feel THAT bad, because you are also a cheater!"
And then it hit me. This is the first time that they are actually communicating. When we first met them, Emma is dying to get out of her house and put some distance between her and her mother. We can say that she married Flap because he was her ticket out of there.
Then they keep making babies, Emma takes care of them, and Flap continues putting his job first. Then both become so estranged, that both take lovers and their only thing is common are their kids.
So my guess is, in that scene in the hospital they finally opened their hearts and they are finally communicating... if Emma tells Flap that she also cheated, then it all reverts back to status quo, because let's be honest, Flap was all about his career and his reluctance to abandon completely his bachelor lifestyle, I mean, he loves his kids, but he loves his freedom as well, that's why he pretty much put the kids completely in Emma's hands when she was healthy, and that's why he gave his kids so quickly to Shirley MacLaine in the end.
So, Emma kept her infidelity in secret to facilitate true, genuine communication between them. Perhaps at some point she should have told the truth, but in that moment she needed the upper hand to avoid going back to the "you vs. me" relation they always had.
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