I started using the new Sprite Atlas in the XCAssets folder instead of having my atlases in the project folder. However I noticed that when I did this my nodes were no longe
This appears to be fixed in iOS 10. The only annoying thing is that you can't have two images that have the same name even if they are in separate atlases.
Edit: this is only fixed in iOS 10. If you're running in iOS 9, there's a massive memory leak that will crash the app.