Resetting the Nether or the End gives everyone fresh terrain (and new structures after an update) without touching the Overworld. It's just deleting the right folder.
Anything players built in that dimension is gone afterwards, so warn them first.
1. Stop the server and back up
Stop the server from the Console tab, then take a backup on the Backups tab.
2. Delete the dimension
Where it lives depends on your server software. Open the Files tab.
Paper, Purpur, Spigot: the Nether and End are separate folders next to your world.
- Nether: delete
world_nether - End: delete
world_the_end
Vanilla, Fabric, Forge, NeoForge: they're inside the world folder.
- Nether: delete
world/DIM-1 - End: delete
world/DIM1
(Replace world with your level-name if it's different.)
3. Start the server
The dimension is generated fresh the first time someone enters it.
The End and the dragon
Deleting the End brings the Ender Dragon back. Players who already have an elytra keep it. If you want the dragon fight but your End is otherwise fine, there's no need to delete anything: placing four End Crystals on the exit portal respawns the dragon.
Player positions
Players who were in the deleted dimension when you stopped the server are placed at a safe spot when they log in. It's worth asking everyone to go back to the Overworld before you reset.
Questions
Will this delete players' inventories?
No. Inventories are stored separately from the dimensions. Items in chests or on the ground in the reset dimension are lost.
Can I reset only part of the Nether?
Not by deleting folders. A tool such as MCA Selector can delete chosen regions while the server is stopped.
Will the reset Nether have new 26.1 structures?
Yes. Fresh terrain is generated with your server's current version, so it includes anything new in that version.