I think California is more concerned about the smog certification than flares. If it is 49 state model never registered in California you may have to pay extra (~$300?) to get it registered, and you need proof of prior residency and that it was registered to you in the state you moved from. Fee goes toward a smog abatement program or something. 50-state model, no problem.
The local police may want some extra cash though and find reason to ticket you, because technically, you are supposed to have flares that completely cover your tires. Technically. If they really stick out, you are at risk of getting nailed, if not, no worries. California doesn't have regular physical/safety inspection programs for passenger vehicles. Just smog checks.