Mobs despawn on 1.9 server when moving dimensions

I upgraded my 1.8.9 world to 1.9. I have a mob farm which works by sending mobs through a nether portal to the nether to bypass local mob caps.

When I run the world in single player 1.9, the mob farm works as intended.
When I move the same single player world onto a locally hosted 1.9 server, the mobs I had sent to the nether de-spawn whenever I move dimensions. This prevents the mob farm from working.