The Nerevarine destroyed the enchantments on the heart, letting it return to its owner.
As for the eating of the world, Aldudagga answers it thus:
"And the Greedy Man always waves his arms about around this time as if to stop me just like you. It is almost as if you two work together to delay me. Is that what this is? Is some other low spirit hiding portions of the world while you two do this thing? Is this why the kalpa-feast always takes a little longer than it did the previous time?"
And then Alduin looked hard into the eyes of both the Greedy Man (far away) and the Leaper Demon King (close up), one of them for each eye of his own, and he knew it was so. These two spirits gulped big, and were caught.
"Oh crap," the Greedy Man said, "He knows my bargain with the king of leapers, I'd better hide under my mountain!" but he thought and said all this too fast and, without thinking, hid under his mountain even though its base had already been eaten and so it wasn't all still there. (This is how the Greedy Man became trapped both in and outside of kalpas.)
"Oh crap," said the Leaper Demon King, "You have found us out, World-Eater! Yes, just after the two bells of the All-Maker's Goat sound the Greedy Man and I and our servants hoard bits and bobs of the world so you can't eat it all. And when the world comes back we sort of just stick these portions back on and so that's why it is all bigger and bigger for you to eat each time.
A similar sentiment is repeated in the Redguard creation myths. Basically, some spirits have found a way to bypass the eating of the world, and Lorkhan (the Greedy Man, Sep) is one of them.