— I know this is a closed report, but this happens to me on Windows occasionally. I think individual layers get bugged after a long while sorta randomly. If you haven't found one, I have a workaround for it. Just make a new layer, highlight everything on the layer that's disappearing, and use the properties window on the side to switch them all to the new layer. Delete your old layer, rename the new one back to the original name and things should work. I've had this come up on a couple layouts, but this workaround seems to fix it.
Most often, though, it's a single object causing it. When things are disappearing, zoom in and scroll around. You'll probably find a place where things disappear, but reappear when that part isn't on-screen. If you delete everything in that region, it usually fixes it, but you can also narrow it down to what is causing it and replace/remove that single object and things usually get fixed.
To show this, I had a place in my game where this was happening. I took a quick, compressed video to show it. I scroll around the layout showing things work unless a certain portion is on-screen. Turns out, it didn't like a 9-patch object I was using (though I've used it elsewhere just fine. No idea). Once I narrowed that down and deleted that object, everything displays properly again.
http://www.adamcreations.com/show/2014- ... 855-41.flv
I just added the objects back in a minute later and things were fine.