Under California law, as I read it (and I've read the law but I'm not a California expert), the employee is entitled to at most 2 separate 30 minute breaks. So the issue of whether you can break up the person's 1 hour break is a non-starter because they are not entitled to a 1 hour break under the law. If you have internal policy, established practice, government administrative code, or a CBA in place saying otherwise, that's a different matter.
My own experience with administering break laws in other states suggests that it's pretty much up to the employer as to when the break is to be taken. The California code does not say that a person can't have their break until after any particular period of time. I can recall in the past situations in which an employee preferred to be let off work 30 minutes early rather than take a 30 minute break in the middle of their shift. That's actually frowned upon in the Department of Industrial Relations Q&A section. Some laws are more detailed than others. For example, in Washington, you can't make someone take their break less than 2 hours from shift start or more than 5 hours after shift start in addition to other specifications about how the break is to be administered.
I don't see anything like that in California 512(a), 800, or IWC wage order no. 1-2001 sec. 11. However, there may be something in regulation that you won't see in the statutes. http://www.dir.ca.gov/dlse/faq_mealperiods.htm
Based on a quick re-read of the meal periods faq for California, I think you are OK with having your employee take one 30 minute break 3 hours into shift and another one later in the day. In fact, in the proposed revision of the regulations, they stipulate that you have to provide a break in the 5th hour of work unless you have already provided one. http://www.dir.ca.gov/dlse/mrpregs.htm