This is exactly the problem I've. However, mine wasn't a system drive. There's definitely a virus that's targeting executables. It just nullifies their sizes to 0kb. I don't think it's overwriting anything.
There's a friend who had your exact problem and i just noticed it was a viral infection. So i backed up stuff and reinstalled Windows. I gave her the laptop before i could finish installing an antivirus and other devices and software that she used; i was
very busy with something else. I told her not to use it yet, but she did. She got the same virus into the thing thru a flashdrive from another friend i think. When i came to finish up, i installed some software normally at first. i used my external drive that
has all my installations in it. It worked at first, but when i got to install other programs later on i noticed they were 0kb. I went back to one of the setups (VLC) that i had installed earlier successfully and noticed it too was now 0kb. I looked all over
the drive and all exe files were now 0kb.
This is definitely a virus targeting executables only. The help i need is how to undo those nullifications. I think the data is still there, as the space reported is still the sam for the total drive, just that the file is being reported as 0kb, therefore
nothing and unexecutable. I tried looking for hidden files, scanned the drive with Windows drive tools in drive properties and scanned for viruses, which is reported ok. The drive has no infection coz and isn't corrupt.