Who's to say it's the same Tingle? Please take a look back at where we first met this fairy-wannabe, which was in Termina, the world of Majora's Mask, as a special reminder to everyone. And what is Termina? A parallel world of sorts full of lookalike characters from OoT Hyrule. Although there is pretty much zero ground I can ensconce this idea upon, I believe that Tingle didn't have to only be in Termina. He could've just as easily lived in Hyrule as, say, the Cucco Lady or the Running Man, even if he wasn't ever seen.
It's possible that Tingle dwelled on one of the higher elevations that were inaccessible in the Ocarina of Time. Maybe it was a mountain peak that he and his brothers (as there is more than one Tingle in Wind Waker) fashioned into what is now known as Tingle Island. That would mean that they were already on high ground whenever the floodwaters deluged Hyrule. As for Termina Tingle, I'm uncertain what happened to him. If Hyrule became overcome by the flood, then Termina credibly was affected somehow as well. In which case it doesn't really matter that Link saved Termina, because it underwent a devastating calamity nevertheless.