every update comes with its own updated edit file, so changes made will be overwritten by the update, this tutorial explains how to keep a custom team after the release of a new update, this works with all game versions, although maybe a little different menu in both versions, newer games...
Depends on if there are any files tied to the hardware that you'd need to dump to be able to run the games. Pretty sure CEMU needs keys for some Wii U games. For the PS2 emulators, you needed to dump the BIOS, I believe.Mr