I have a named zombie in a minecart for my iron farm. He was high up in the sky and safe so he did not die. When I replace the zombie then after a while he disappears again. 

I have included 2 screenshots from the minecart that should be holding the zombie and a view from above so you can see it should be save.

I have checked my logs and couldn't find much but I did have some errors:

[14:08:36] [Render thread/ERROR]: ########## GL ERROR ##########
[14:08:36] [Render thread/ERROR]: @ Pre render
[14:08:36] [Render thread/ERROR]: 65539: Invalid mouse button 99

and

[14:08:18] [Render thread/WARN]: Received passengers for unknown entity

I have uploaded the log, I recreated it succesfully, I was AFK at my mob farm which is in the near area and my zombie disappeared again.

On my singleplayer world I play with Fabric but I have the same issue on my vanilla server.