On my server, we just pruned the end because we have a world border and ran out of cities. Everything seems to be working great now, except for one thing: End gates are spawning above the void. This is impossible when looking at the game code, so our guess is that the gate locations are saved somewhere in NBT data. Naturally, I went looking around, but I didn't find anything, so I was hoping someone here could help.
In short: Is there a way to force end gateways to regenerate correctly (and possibly delete the old ones)?