Yes, you can fight Braev (and any of the other asterisk-bearers, with the exception of the one you won't encounter as a combatant until chapter 6) in any of the alternate worlds. However, because there are various differences between these worlds, events will not play out exactly the same way each time, and you'll occasionally find that certain side-quest bosses have moved around. The positions of these encounters will always be marked on your map by those blue "!" indicators, though.
If you don't find the character you seek where you'd expect them to be, pay attention to little things that might have changed between worlds and mess around with conditions a bit (for example, entering a location at night instead of during the day). If you still can't find them in the same location, it's possible that they've grouped up with other asterisk-bearers elsewhere; they do eventually get smart and gang up on you in later chapters.
EDIT: In Chapter 6, for example, Braev is not found at the top floor of Eternian Central Command, but is found elsewhere during a side-quest for a different asterisk. Just to be safe, I've placed the details of the process for finding him in spoilers below; if you don't mind finding out who has the last asterisk (as mentioned above) or learning how you go about getting it, mouse over the gray box to make the text visible.
After having Sage Yulyana repair Agnes' vestal garment in Chapter 6, return to his hut and read the note on his table. You can then begin the side-quest for the Conjurer asterisk, which belongs to Yulyana himself. The party must meet the sage in four locations, where an event occurs that presents an interesting conflict to each of the party's members in turn. (I won't spoil the events for you, as it's much more entertaining to see them yourself.) At one of these points, you are directed to Eternia's medical tower, where Edea's mother is located. Braev will be there as well, and after some dialogue, you'll face him in combat.