Is it possible that WorldBorder may be the culprit in this. On our server, we used WorldBorder to pregenerate the world with a radius of 7500. We still use the plugin to maintain chunks outside of the border to keep world size down.

Issues:

• Any village within the border is empty (no villagers)
• Ocean Monuments exist, however, no guardians spawn. using //regen via worldedit resolves this until chunks are unloaded and reloaded.

Thanks for consideration