Downloaded world has sections that I have built missing

I have downloaded the world off the server that I have been playing on, it seemed pretty normal at first, but when I was in the nether, one of my nether highways was cut off and my entire wither skeleton farm wasn't were it was supposed to be, instead it looked like it reverted back to when I didn't build anything at all, and seemed like I visited those chunks for the first time.

I have just done that, and it seems to have fixed the problem. Thank you.