They still appear in the waypoint menu but are entirely gone from the map, world, and screen edge.
This either happens when leaving and re-entering the end or after logging out; Not sure which (only just noticed it on my survival world when looking for my end city waypoint)

I've created waypoint in The End, several times reloged and reentered to The End. Waypoint don't gone.

Try to increase waypoints render distance in the map config.