If I was Skylar, I would have moved away. It must have been really hard for Walt Jr so I would want Holly to grow up where nobody knows who her father was. She might have, as it'd explain Skylar not being there to support her sister in those hearings and courtroom scenes...
She got her deal (as Francesca told Jimmy) and we know she had moved out of the abandoned White house by the time of the events of Felina. Wouldn't be out of the realm of possibility for the FBI to relocate her and the kids out of the Southwest just in case someone came looking (since the Feds never really knew the full extent of Walt's empire and how many different parties he had gotten involved with, like the neo-Nazis; who's to say Lydia was the only person at Madrigal with their fingers in the meth ops?).