I haven't used Linux in a very long time so there could be some file incompatibilities I'm not aware of, but if you don't know how to find the folder (Appdata is hidden in Windows by default, personally I kinda get annoyed whenever I have to go to it for anything) you can start up sm64coopdx, then click "options" >> "misc" >> "Open appdata" to pop the folder right open. From there, you probably want to go up one level to your roaming folder, then copy your sm64coopdx folder to your USB drive. Then just paste it into roaming on your new OS.