What kind of a process would it be to keep a save file if you are moving from having the game being played on a cartridge you personally own to a pirated or legally obtained digital copy if you are doing it in the emummc?The only reason I don't recommend the latter is that involves using homebrew and CFW which might put you at risk for being banned.
I updated emummc in Hekate and still got the missing data message so need to find a new solution to try and play the Pokemon games.