Pathless Plain (The island where you get Cobalion, Terrakion, and Virizion.) only appears while you are soaring if you have three Pokemon in your party with 510 EVs. When you went to buy Pokeballs, you might have changed your party so that there weren't three Pokemon with 510 EVs. So yes, the island does reappear, as long as you have three Pokemon with 510 EVs on your team.
(As Sumwun said, if you defeated Cobalion, you will probably have to defeat the champion again for it to reappear.)
Hope this helps!