Nether and End have been reset

So when I came on my server tonight we found out that all the plugins had been deleted. It was a bit annoying so we downloaded the world file and rolled back to yesterday's backup. When we came on, everything was fine except for a little progress lost. When I went to the nether, however, it was empty, and our rail system was completely gone. I'm assuming that the same thing happened to the end. How did this happen and how do I go about restoring just the nether and End files from another backup that I downloaded onto my computer.

Thanks

Quote from Roman

Which software and version is installed on your server?

PaperMC version 1.15.2

Every time I try to restore a backup, the nether and end get reset each time

It seems that my nether and end have been reset, and there's no way to get them back