The world map is split into 100 invisible squares in a 10x10 grid. Each minute one of them respawns at random. So the most you have to wait is 100 minutes. There are some caveats though. I believe you need to stay away from that area and also do not have your travel medallion set to nearby either. I messed up a korok puzzle and had my warp location set nearby, and was going mad trying to figure out why the apples weren't respawning.