"Hero of the Village" effect (and any effect that lasts forever) gets cleared when using the Exit Portal in The End.

I just got the hero of the village and went to the end to repair my gear. When I entered the exit portal, the effect disappeared. So I tested it. It turns out that if you teleport yourself from the end to overworld using commands, the effect stays. It is only when using the exit portal that it clears your effects.