The first (Decoy) and third (Hail Mary) episodes of this season were filmed at the end of season 10. NCIS Los Angeles has done this kind of production scheduling before (and so has JAG). So Barrett's availability is based on filming done last April (at the end of shooting for season 10), not July (the beginning of shooting for season 11). And he wouldn't have let them know he was unavailable; if he was under contract (I assume he is), he would have negotiated the time.
"Letting" the show know about unavailability is something that happens with issues that can't be re-scheduled, like pregnancy (DR), serious/terminal illness (Miguel Ferrar, Linda Hunt), funerals, arrests, and so on.