The couple have been married since 1995 and have three children together.
People.com said Phillips, 42, filed for divorce last Friday in Santa Barbara, but then changed her mind and withdrew the documents.
"They're not getting divorced," her manager, Lizzie Grubman, told People.com. "She filed and withdrew. They are going to work out their issues."
Phillips is best known as a member of the pop group Wilson Phillips. She is the daughter of the late Mamas and Papas singer John Phillips and the half-sister of actress Mackenzie Phillips. The family made headlines late last year after Mackenzie publicly claimed she was repeatedly raped by her father John Phillips as an adult during the course of a decade.
Baldwin has starred in the films "Flatliners," "Backdraft," "Sliver" and "The Squid & the Whale," as well as the TV show "Dirty Sexy Money."