Since destroy kind of destroys "everything", a cheap and simple solution when all you really want is to just "reset the data". Resetting your datasets to an empty array will work perfectly fine as well. So, if you have a dataset with labels, and an axis on each side:
window.myLine2.data.labels = [];
window.myLine2.data.datasets[0].data = [];
window.myLine2.data.datasets[1].data = [];
After this, you can simply call:
window.myLine2.data.labels.push(x);
window.myLine2.data.datasets[0].data.push(y);
or, depending whether you're using a 2d dataset:
window.myLine2.data.datasets[0].data.push({ x: x, y: y});
It'll be a lot more lightweight than completely destroying your whole chart/dataset, and rebuilding everything.