I would be curious to know more about how you are doing this. Maybe
Microsoft fixed this since I last used WSL, but if they didn't then you may be sitting on a ticking time bomb, see: https://blogs.msdn.microsoft.com/commandline/2016/11/17/do-n...
From linked post: Note: Your "Linux files" are any of the files and folders under %localappdata%\lxss - which is where the Linux filesystem - distro and your own files - are stored on your drive
It does say later on that storing files on windows filesystem and accessing it via /mnt/c is ok
When I set up a new machine, the first thing I do after installing WSL is to remove all directories from my home folder on the WSL filesystem, then symlink the directories in my home folder on the Windows filesystem. This way I can avoid accidetally saving files within the WSL filesystem, but don't have to prepend all paths with /mnt/c/Users/me (almost all my work occurs within my home directory).
There were a couple of very minor hiccups in its early days, but for the last year I haven't had any issues with it at all and it certainly makes developing on Windows a whole lot more convenient.