Once I have encountered and defeated Cobalion, Virizion and Terrakion, will I have the opportunity to capture them at a later time?
Yes. Ever since Ruby & Sapphire, if you knock out or flee from a legendary Pokémon or (starting in HGSS) a fixed-location Pokémon like R36's Sudowoodo, the Pokémon will reappear after the next time you defeat the Elite Four & Champion; if you defeat them again, they'll reappear again after you enter the Hall of Fame once more, and so on until you finally capture them. In the case of the Swords of Justice (Cobalion, Terrakion, and Virizion) in B2W2, according to Bulbapedia, they all reappear in the same location at a higher level: while they are all level 45 the first time you encounter them, if you don't catch them the first time, they go up to level 65.
Very sure you run into them twice, if you do not capture them the first time they will appear later at a higher level in a different location. I know they have the answer for sure on Serebii.net. On that site just find Black&White 2 on the left and look up event pokemon on the right I believe.