LE is a complete OS not an App, so you cannot run it from within Windows. And nano is a Linux text editor; like notepad, but run from the Linux command shell, it's not a GUI app.
It's hard to comment on what's happened, but either the SD cards are old/bad/dying which leads to corruption and issues or perhaps you're powering off the machines without clean shutdown and causing filesystem problems on the cards. Linux is a lot more sensitive to that kind of thing than Windows; it will fail loudly and early whereas Windows sort of blindly continues giving the appearance of normal while secretly trashing your data.