Get the files transferred from what? Your Win11 laptop? Because it's reasonably likely that the files won't work properly if transferred- Windows executables don't just work on Linux.
Also what games specifically are you trying to play? For BG3 you'll probably need to find the Linux version or get Proton set up. For TotK you can probably use most of the same files, but you'll need a new emulator install. There's roughly a thousand Switch emulators so pick your poison and following the install instructions.