I had the same approaching the Heart and Sould nebulae. After half of the jumps I made, there was no Heart. Soul was always there.
The suggestion someone made that it's to do with one nebula hiding the other sounds likely. Approaching the galaxy core I find it funny that nebulae are surrounded by pitch black space, while the rest of the screen is covered in the yellowish glow of the Core. So it looks like the nebulae are drawn opaque, not transparent.