I think it was actually a "coincidence", so to speak.

The food in the sacks was in an undefined state of being either rotted or not. Rand cannot change this, we never see him take rotten food and make good food from it, the sacks that Iralin had already opened remained full of rotten food. However, it just so happened that the sacks opened after Rand's arrival all contained good food. It is "coincidence" in that Rand did not actually change the state of the food, but its state entirely depends on Rand's nature at the time. The sacks that were opened when Rand was consumed in darkness just so happened to have bad food. The sacks opened when Rand had reached enlightenment just so happened to have good food. The food can be considered both rotten and good until someone actually looks at it, at which point its state becomes permanently one or the other. Schrödinger's grain?

Same with the apples, Rand did not unrot the rotten apples, the apple tree just grew some more.