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I just assumed windows and your standard emulator. ;) I think this will help https://www.youtube.com/watch?v=_F6NMYdrjTY It will tell you where your saves are and the last part should help you start from your previous save.
^
Same way you did originally.
You want a fresh version of the game. Don't patch over patches.
Then all you have to do is copy and paste the save file to the folder with the newly patched game.
Just wanted to drop by and say I am loving the hack, it gives a new meaning to "got to catch 'em all".
Bug: Not sure if this is related to the already know freeze issue about emulators and if this has been reported before I apologize in advance but.... When in the rock tunnel the game tended...