She was always, at least publicly, involved with the project. There were pictures of her playing with Bekka and Dave prior to Billy's return, and there's the one full band picture. In every interview they gave, she was still mentioned as being the Brian Wilson of Fleetwood Mac. The only songs that she's definitely not on are the ones where Steve Thoma is listed as keyboards, as opposed to additional keyboards.
Maybe she started the project with the band but decided to pull out midway through, maybe around the same time Richard Dashut left the project, but was forced back into it for contractual reasons. I have no idea because there's photographic evidence she was there from the start, was always mentioned in interviews, and I've never seen anything to suggest that she wasn't involved.