Microsoft's platform design is generally open enough to allow you to do dumb things. This is a good thing, because you can reg-hack your way around problems with the OS. But like editing the registry, doing so is very much at your own peril, it's really not designed to be tampered with by users.
People who enable visibility on protected system files and then act upset that messing with protected system files breaks things, are the sort of reason we don't give out admin rights where I come from.
I'm a 20+ year Linux user. I use Linux tools to find things and to navigate places. I guess if I were a Windows user, who does things in the usual Windows way, I might have received a warning of some sort.
I'm just saying it'd be cool if there were a warning somewhere in the docs about this issue. It wasn't something I expected. I mean, I don't have to worry about editing "Windows" files on my Linux system with WINE. And, I'm able to mount my Windows partition from Linux and edit files without fear of harming things. I assumed things worked the same way for WSL. It was a wrong assumption, but I don't feel like it means I'm stupid to have made it, based on the knowledge I had at the time.
If you find any docs about this folder from Microsoft, you will find that they do warn you about exactly this.
"Interoperability between Windows applications and files in VolFs is not supported." -- Microsoft
It's no big deal, really. I didn't expect miracles, and it all works much better than I expected. I wish the interop were better, but I'm pleased it's even something Microsoft is trying to do.
https://blogs.msdn.microsoft.com/wsl/2016/04/22/windows-subs...
But I suspect they specifically wouldn't mention it because it's an implementation detail people aren't supposed to know about or look into. The problem might have been more widespread had they actually said "Don't change anything in this specific hard to find hidden/system protected folder"
What, like this bit in the install instructions page: https://msdn.microsoft.com/en-us/commandline/wsl/install_gui...
After installation your Linux file system components will be located at: C:\Users\<Windows user name>\AppData\Local\lxss\ This directory is marked as a system file which are hidden by default. Accessing this location directly is not advised due to caching between the Linux and Windows file systems. Check out our blog post for more information.