All homebrew-related activities should be done on emuNAND, not on sysNAND. Leaving even a single trace can get you banned. That said, there’s no clear definition of what actually does or doesn’t leave traces. Using a save manager to import/export save files doesn’t seem to, but I still wouldn’t recommend it.
A safer approach is to mount the sysNAND partitions via Hekate using ninfs, manually export the save files from /save and /saveMeta folders, decrypt them with hactool, edit them with PKHeX, and then import them back by doing the reverse process.