It seems that the official download mirror was hijacked for Classic Shell and it redirects to a version that overrides your master boot record on your hard drive
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Wow thats nasty! Thanks for the PSA
Like it says in the link, ClassicShell is fine if you don't update through FossHub. And this is easy to fix. You can use TestDisk.
It's also probably possible to fix this if you have a Windows Repair Disc. Then you'd have to access the command prompt and type bootrec.exe /fixmbr
It should do the trick.
But this also seems to fuck with your usb. I'm not sure how that can be repaired. If somebody knows more please share your knowledge.