This is an issue that I haven't seen before.
Hate to say it, but a factory reset would probably fix it.
You could also try dirty flashing (remove the -w flag in the flash-all) the factory image
That happens to me occasionally perhaps once or twice a week. I keep another weather app on a far home screen for when that happens and just scroll over. It usually comes back within a few hours. If you're rooted then this might not apply.