Steps to Reproduce:

1. Place a dragon in a Dragon Soul Crystal.
2. Release dragon from Dragon Soul Crystal.
3. Mount dragon and fly around, it will disappear after a while.

After release and install of holiday patch went around exploring to see the new holiday skins and tame some.
Found one of those nether portal ruins down in a ravine. Put the RR I was riding in a crystal and went down and gathered items. Afterwards released dragon and flew off to continue looking for wild dragons. After a few minutes the RR just despawned, dropping my character to the ground. Went back to where it had been placed and released from a crystal and it was not there. Checked base and it was not there. Have had no issues using crystals before update.

While waiting for videos to upload to youtube I was able to replicate the bug using an alpine and another RR.

Playing single player, game did not crash so no game log.

MC Version 1.16.3

Video of finding portal ruin and putting RR in crystal, gathering weeping obsidian, releasing dragon and flying way.

https://youtu.be/6EjF9fo8XZU

I periodically stop and restart recording so the videos don't get too big and unplayable, I did such a break just before dragon poofed. Video of RR despawning.

https://youtu.be/epegPYrJiEU

Same problem. My Red royal has been despawned.
1.16.3-1.2.9

Potential Cause:
Something related to "Vehicle Moved Wrongly".

Ive tamed 3 Alpines and they all despawned in mid air and i died literally 3 times wayyy far away from my spawn ._.

If I can figure it out I'm definetly going to be releasing a patch for this..

I have the same problem recently. When you put the royal red in the end when releasing it from the soul crystal, they will disappear after a short while. The world is hardcore, and I have never been so glad that I've created a backup beforehand.
I have no screenshot of this because the bug was almost instanty executed.
But the bug is real. I'm not sure catching releasing a dragon from a soul crystal is the wise choice fr now.

The version where the bug was executed on my pc is 1.16.4.

Edit 2
Ok I'm not sure if this will help out but I think I know what is causing the bug.
Ok so the bug can be executed but only if you put the royal red on a soul crystal and after saving the game. I think the game is identifying the dragon as an item only and because of that, it deletes the code of royal red from the code when it's inside the soul crystal, therefore when reloading the game, poof, it's gone.

I can't explain it worse or better but either way, I think these are one of the possibilities.

I mean, I was still able to catch and release the royal red in and out of the crystal before saving the game so...

Ok 3rd edit.

If you want your dragon to NOT disappear, release it from the crystal BEFORE you save and quit the game. Also you can take down my issue from 21 days ago, it's all good now, ty.

This same issue has been very prevalent on the modded server I'm hosting for my friends. Its happened to alpines and butterfly levis many times over the past few days. From the server logs I can see two possible causes for the bug. The first is an issue with the "vehicle" moving wrongly which usually occurs when the server is behind on ticks and is trying to catch up. The log says "Alpine Dragon (vehicle of [player's username]) moved too quickly". The second has to do with duplicate entities being loaded in different dimensions such as the nether and end (I think). The console will log "Trying to add entity with duplicated UUID" followed by the entity id. I can provide exact details of the console if necessary but I would rather not share it publicly just because I'm port forwarding the server and don't want to accidentally leak my ip or something.