Since the new update, Autosaving from both the 1-5min timer, and 'save when closing file' have been very finicky.
I typically work in pretty big canvas sizes, so it's not really that much of a surprise for me, with canvases of 100+layers on canvas sizes of 2000x2000 300dpi to 5000x5000 300dpi. I'm aware that the iPad has a function to automatically close apps when they start to use too much memory.
That said, since the recent big iPad update, autosaving has become far more inconsistent in actually saving, and I've actually lost a canvas to this issue now. I recommend turning it off, as well as turning off >save when closing file, AND to save before you swap apps away from ASP. Swapping apps also seems to cause issues with saving, for whatever reason. So, here's a heads up.