I did this to reduce chunk loading time and memory use, and to make the server lag less than it used to.
The server is run by a server hosting company (WiseHosting). It uses Paper, with these plugins:

https://www.spigotmc.org/resources/maintenance-bungee-and-spigot-support.40699/
Chunky
SimpleVoiceChat
ProtocolLib
LibreLogin

When we joined the game, We found the nether dimension regenerated. Every structure and portal we had build was removed.
The end is even worse. The end had been regenerated and there was no dragon portal. It was missing. I even checked under the island, but there was no portal.
After checking the logs, I didn't find anything. I suspect that the culprit behind this incident is Chunky.

I also have to mention that at one point, because I
set the Radius at a very high number, I smashed the 10GiB Limit that they provide. I don't really think that they could have deleted the end and nether dimensions to free up space, but I think it's also important to mention.
Here are a couple of screenshots

I'm sorry for your loss, but this isn't possible. Chunky does not randomly delete worlds. The fact that you pre-generated chunks beforehand can only be a coincidence but by no means the cause, unless you or your host deleted the files afterward (some hosts have policies around how much disk space you are allowed to use, you may want to check them or ask your host. Aside from that, my advice to you personally is to revert to a prior backup, or get in the habit of it so this doesn't happen to you again.