[ryl00]

From https://blogs.msdn.microsoft.com/commandline/2016/11/17/do-n...

Therefore, be sure to follow these two rules in order to avoid losing files, and/or corrupting your data:

DO store files in your Windows filesystem that you want to create/modify using Windows tools AND Linux tools

DO NOT create / modify Linux files from Windows apps, tools, scripts or consoles

Remember: There's a reason we gave the %localappdata%\lxss\ folder 'hidden' & 'system' attributes

[daeken]

That's talking about manipulating files in the LXSS filesystem from Windows tools. There's no problem with doing everything on your Windows mounts, assuming you don't mind everything getting +x.