Whenever I try to download any branch of UE4 as a ZIP file from Github, It only downloads the engine folder and it’s contents, along with gitignore and gitattributes. The Setup.bat file and all other files in the root UnrealEngine directory are missing. This happens if I download from my fork and when I download from Epic Games directly. I’ve downloaded the source several times before with no issues, so I don’t know what changed. I don’t know if the Git client causes the same problems, but I can’t use it anyways because it is absurdly slow. Anyone know what to do?
Virus checker deleting them when you extract?
I only have windows defender at the moment. It shouldn’t do that. The files aren’t there before I unzip either. They never downloaded at all it seems.
Weird! I wonder if your browser or your ISP’s web proxy is caching the wrong ZIP file. Try selecting a different branch version (ie. 4.10.1 instead of clean-master) and download the ZIP for it and see if that helps. Or try a different browser!
Let me guess, you are using windows 10? 
try unzipping with 7zip instead.
Windows 10 does that??!! facepalm
Actually not Windows 10. I thought it was that first, but than I noticed that same thing is going on in Windows 8.1 too internal zip tool. Github must have changed something when zipping, that 7zip reads right but Windows does not. Or there is something different going on that I have missed altogether.