I'm making a scientific animation where I have one molecule enter the scene, undergo a reaction, and appear to change into another object. Right now these are two separate objects. The molecule that enters has a pink sphere that morphs into a slightly larger gray sphere. The gray sphere is already in its proper location, doesn't move, and is disabled in renders until just before the reaction finishes. Then, when the reaction on the pink sphere is almost finished, I toggle the gray sphere on. The gray sphere has a mixed shader that starts out fully transparent and ends fully gray. I want to show the transition from pink to gray sphere, with the larger gray sphere slowly eclipsing the view of the pink one (as the pink one is located fully inside the gray one). I'm repeating this reaction multiple times with object copies throughout the animation and this problem only seems to occur sometimes and I can't figure out why. I'm posting two examples. In the problem example, as soon as the gray sphere is enabled in renders, the pink sphere disappears from view (both in Eevee and when I render a frame). The pink sphere is fully inside the gray sphere (because I want to show the transition) and the gray sphere is fully transparent. I'm not sure what the issue is. I'm just copying the material for the gray sphere for each new reaction and keeping the pink sphere's material exactly the same. Sometimes it works and sometimes it doesn't. In looking at the ones that work and ones that don't I can't seem to find a difference. To be clear, I'm using Blender 2.8 Eevee, using Alpha Blend with Show Backface unchecked for transparency, and not using render layers.
Can you help me figure out how to make this work consistently?