Entities disappearing

We're currently (on 1.16.1) experiencing disappearing entities (since 1.14.*) on active chunks. There is a chance to fix by restarting the server before the appropriate chunk gets rewritten (e.g. by a block-change) into memory/onto harddrive, but the problem re-occurs.

The problem persists in all worlds (some of them have been carried around since minecraft beta [yes, we're that old]), but even new ones which have been created recently by custom world generators or vanilla generator.

We already tried to disable plugins we had in mind to mess up with entities without effect.

The logs do not say much about entities, except:

2020-09-24-2.log.gz:[09:02:58] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:58] [Server thread/WARN]: Skipping Entity with id minecraft:skeleton
2020-09-24-2.log.gz:[09:02:58] [Server thread/WARN]: Skipping Entity with id minecraft:zombie
2020-09-24-2.log.gz:[09:02:58] [Server thread/WARN]: Skipping Entity with id minecraft:pig
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:chicken
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:chicken
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:02:59] [Server thread/WARN]: Skipping Entity with id minecraft:cow
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:skeleton
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:creeper
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:bat
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:sheep
2020-09-24-2.log.gz:[09:03:00] [Server thread/WARN]: Skipping Entity with id minecraft:pig

Unfortunately it does not tell which world is affected, and I don't have a clue what the meaning of that message might be. However, it does not to seem be related to the entities that disappear.

This is our list of plugins:

[12:27:40 INFO]: Plugins (67): AntiCreeper, Bedrock*, BKCommonLib, BlockDetector*, BungeeTabListPlus, Chairs, ChatControl, Citizens, CleanroomGenerator*, CNBase, CNBeam, CNChest, CNDeath, CNHorses, CNInventories, CNShop, CNVote, CNZone, CommandBook*, CreeperHeal*, dynmap*, Dynmap-WorldGuard*, EmeraldBank, Essentials, EssentialsAntiBuild, EssentialsSpawn, ImageMaps*, ItemEdit, ItemNBTAPI*, LBStats*, LibsDisguises, LogBlock, LuckPerms, LWC, mcMMO, ModReq*, Multiverse-Core, Multiverse-Portals, NullTerrain*, OpenInv, PlaceholderAPI, PlayerScan*, PluginList*, PlugMan, ProtocolLib, Quests, RebalanceVillagers, RecipeManager, RocketLift*, ServerSigns, Shopkeepers, SignEdit, Slap-Pro, SuperVanish, uHome*, Vault, VentureChat, Votifier, VoxelSniper, WDLCompanion*, WeatherReducer*, WorldBorder*, WorldEdit, WorldEditSelectionVisualizer, WorldGuard, WorldGuardExtraFlags, Yamler*

The plugins Bedrock, CNBase, CNBeam, CNChest, CNDeath, CNHorses, CNInventories, CNShop, CNVote, CNZone and RebalanceVillagers are our own ones, they do not mess up with entities on that large scale. We already tried to disable some of them, and we also disabled others, again without effect (entities still disappeared).

My guess is that, when an error occurs (most likely with an entity) on a particular spot (chunk), all other active chunks around this one got affected too and all entities vanish. If we manage to restart fast enough without any world save at these chunks, the entities are back. If not, they are lost. 

Most times we only know about missing entities when a player logs in, plays/sneaks around (makes dumb stuff) and yells "z0mg my entities are gone". But we don't know if the entities are disappearing at that very moment (user logs in, makes stuff) or if they have already been gone before (which I don't believe in).

However, this is annoying. If you need more information, please tell me.

All the best