Garner was on a work trip to New York City when she approached Shookus about the fling. “Lindsay refused to back down or quit the affair,” says a source.
Responds a source close to Shookus: “Jennifer and Lindsay do not have any relationship.”
Multiple sources have told PEOPLE that Affleck and Shookus started having an affair in 2013, two years before the actor and Garner announced their separation. Shookus was also still with her husband Kevin Miller, then a fellow SNL producer. The two split in 2014.
However, other sources close to Affleck and Shookus maintain that the two were just friends and didn’t date before their respective separations.
Sources also say Garner spoke to Shookus’ ex about the affair. After appearing on an episode of Late Night with Seth Meyers, where Miller is now a supervising producer, Garner sought him out for a conversation.
The first source says she showed him text messages between Affleck and Shookus, adding, “she had proof.” (Miller and Shookus were already split at the time.)
For much more on Affleck and Shookus, pick up this week’s issue of PEOPLE, on newsstands Friday.
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Affleck and Garner announced their separation in 2015 after over a decade of marriage and filed for divorce this past April. They have continued to closely co-parent their three children — Violet, 11, Seraphina, 8, and Samuel, 5.
“Ben and Jen continue to be dedicated to their family and kids,” says a source who knows Affleck and Garner. “They have been separated for two years now and have never strayed from that dedication. They do it better than anyone.”
Shookus married Kevin Miller in 2010 and the two share a daughter. “They’re both really good friends still,” says a source close to the situation. “They’re both good, devoted parents. Lindsay and Kevin’s marriage didn’t end over infidelity. There were issues they couldn’t resolve and they realized they were better as friends than together.”
Garner is handling her ex’s public relationship fine, sources have said. “Nothing is new for her here,” says one insider. “She’s in mama-bear mode.”