This happened to me -- the option to swap Win and Fn disappeared from the BIOS. I "fixed" it by going into the BIOS and resetting to optimum defaults. The option is still missing.
But the next time Windows started, the "MSI Center PRO" app started up and now instead of only offering backup/restore, it showed some "Initializing" popups then showed a window with a Gear icon (Settings) in the sidebar on the left. This has a toggle for "Switch key" which allows you to toggle the swapping of Win/Fn.