I'm still having this issue with 19w09a.
Here are images of the same spot after restarting the server:
[media][media][media]I'm having the same issue in 19w08b. I'm playing on a server and I have observed that if I restart the server or if I go to the nether and come back, other entities disappear and appear sometimes duplicated, randomly.
I'm having the same issue in 19w08b and I have observed that it happens when a player is near the entities.
I have a villager breeder and on loading the chunk where it is, the messages start to spam on the console. Also sometimes the entities disappear (villagers, cows, wolves, item frames).
I restarted the server several times and logged in at the same chunk, and everytime different entities appeared and disappeared, sometimes duplicated (what lead me to believe that the keeping entity warning is related to causing it to not load properly)
Yes, it's like there's nothing there when they're not appearing, they're probably not loading at all.