I'm currently running a vanilla server in 19w03c on a world that was created in
1.13.2 it was updated in the following order: 1.13.2 - 19w02a - 19w03a - 19w03b - 19w03c.
I'm pretty positive that it happened because of the server version upgrade.
When any one of the players travels out to load new chunks then the console starts
getting spammed with the "Keeping entity that already exists with UUID"
it starts getting overloaded and then finally it crashes, unless
you somehow manage to tp the player away from the new chunks first.
The only thing I care about is our progress on the server, that means items
and builds, I don't care about XP and animals/villagers since that's easily regained with creative.
I did a lot of research about this bug and I've found out that tons of players
are affected by this game breaking bug, yet Mojang still haven't released a fix for it,
keep in mind this bug has been in the game since 1.7.5 possibly even before that.
I haven't found a fix anywhere I've looked. For some reason, no one is even assigned
to fix this issue on bugs.mojang.com as seen here MC-95649
I've tried the following:
/tp (UUID) playerName and then kill it manually.
Using all the commands above in the console.
Turning NPC, monsters, animals to false and set difficulty to peaceful in the
server properties, boot the server and use the /kill @e command above
until it said no entities found then reverse the settings and boot again.
Donating to Shroud.
Copying the world file to a new server folder and booting it.
What I can't do:
Use the MCEdit filter that Marcono1234 created to deleted or rename the
UUID's because MCEdit doesn't support 19w03c.
Go back to 1.13.2
Download forge and use the mod World Utils to try and delete the duplicated
UUID's, because forge doesn't support 19w03c.
Get a refund for the Shroud donation.
Seeing there's no release date for 1.14 I don't see waiting for the update to be released as an option either.
The only thing that fixed it was, of course, to delete the world and letting the
server re-generate one but obviously, that's not an option.