After transporting entities back form a spatial storage cell all entities become invisible (mobs and items entities), you can still pickup items but can't interact with mobs
Only tested in SP
No idea why, maybe they are not correctly registered to the renderer after being moved?
optifine and betterPVP installed possibly ? they had an issue with chunk updates and entities and players disappearing
Probably, because if you reload the world they reappear. And also if you go with the entities to the pocket dimension they render correctly.
I'm using the Direwolf20 1.10 pack with no optifine or betterPVP. I'll try to test in a clean install of just AE2
Edit: Just tested and the bug still exist with just AE2