A source close to Shookus denies these claims. "They’ve been friends for a long time," the source said. Another source close to 44-year-old Affleck previously told ET that things only got romantic after his separation from Garner in 2015.
ET has reached out to reps for both actors.
According to our source, 45-year-old Garner also talked to Shookus' ex-husband, Late Night With Seth Meyers supervising producer Kevin Miller, about the alleged relationship when he produced her segment during her appearance on the show in March 2016.
"Kevin had heard rumors that there was something going on between Lindsay and Ben but did not know many details about the affair," the source says. "Jen and Kevin had a conversation about the affair and Jen told him everything.”
As for how this may have impacted Garner and Affleck's relationship, our source says there were multiple issues that led to the demise of their marriage.
"There were a bunch of things that broke up Ben and Jen's marriage, but cheating was definitely the main factor that drove Jen to finally leave him," the source claims. "It's something that was very difficult for Jen to deal with."
Affleck and Shookus eventually reconnected in September 2016, according to the source, when the 37-year-old producer met up with the actor at the Four Seasons Hotel in Los Angeles while he was promoting his film, The Accountant.
"It is early on in the relationship but they are very happy together," a source close to Affleck previously told ET. Another source adds, “Ben and Lindsay’s relationship is new and they are taking it slow."
These days, the source says Garner is keeping the focus on her three children with Affleck -- Violet, Seraphina and Samuel -- and isn't "embarrassed" over the situation.
"Jen is trying to move on with her life. Jen is very strong," the source says. "She is not embarrassed about this at all. Jen isn't focused on dating at the moment -- her number one priority is her children and making sure they are OK during this."
Garner has been photographed multiple times hitting the gym in Los Angeles since news of Affleck's new relationship broke, giving a big smile to the cameras. Watch the video below to see how she's staying away from the drama, as Affleck's new romance goes public.