My realm has been experiencing this behavior for several years. I finally got fed up and wrote my own application that successfully downloads my 3GB realm every time without fail as a .mcworld on Windows PC.
The issue seems to be with the chunk the end gateway resides in, cause I have brick scaffolding that will also regenerate in the chunk the end gateway / end tiny end island regenerates.
My realm has been experiencing this behavior for several years. I finally got fed up and wrote my own application that successfully downloads my 3GB realm every time without fail as a .mcworld on Windows PC.