Flux OS is a virtual system overlay made in Visual Studio. That means that this is not a real Operating System but its actually just an application that runs in Windows to make everything look better and give more functions. Flux OS will not change anything to Windows and can be closed at all time to go back to the normal system. When restarting your computer, you're also back in Windows.
Its posible that there are some bugs in Flux OS. Please report these bugs to make Flux 2 better.