When you return from abroad and your passport is scanned, Homeland Security doesn't see your criminal record. However, when a defendant warrants on a case, the prosecutor may alert Homeland security which would cause a passport to be flagged when scanned.
Prosecutors do not typically bother with that for misdemeanor charges, but they are likely to in the case of a felony warrant. Speaking for myself, over the years I have had a handful of clients stopped at the border for a warrant and extradited back to New York.
Do I think your boyfriend is likely to be arrested upon his return when he goes through immigration? Yes, I think it's very possible, and if he flies into a state other than California, he will likely be held there to await extradition. Does that mean he shouldn't return?
Well, the longer he's a fugitive the worse his situation will get. At this point, since I imagine you have plans to return within the next few days, he may actually get back before his passport is flagged, but of course, I cannot guarantee that.