I have a world that was created in Vanilla 1.9.2 and moved to Spigot 1.9.2. Recently, I moved over to Spigot 1.11 and found that at least 3 of the End Cities did not spawn correctly (missing parts of the builds) and/or are missing any loot in the chests, no elytra, no potions in the brewers.

Here is a list of the plugins I have loaded:

AsyncWorldEditInjector, CoreProtect, WorldEdit, ChopTree3, AsyncWorldEdit, SuperSmelter, VoxelSniper, LockedItems, PermissionsEx, AddLight, SinglePlayerSleep, Gravestones, Gringotts, Vault, Catacombs, SilkSpawners, SignShop, SignShopGuardian

If this is due to a failed version of Spigot, how do I get the cities to be re-generated after I upgrade Spigot?