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Yes, there's several versions of FF6. There's at least 2 versions of the english SNES ROM, and you can easily find them on the internet if you know where to look - the differences will be the version number since the newer one will obviously have some bug fixes in. Obviously, Game Genie codes might change/stop working as bugs get fixed, or maybe new codes start working. As a programmer, I very much doubt missing out or changing one line of code is enough to completely remove all traces of a possibility of an alternate ending for a character which will need programming to draw the scene and what sprites to use, how to move them, and even have dialogue in, etc.

What's more, lots of people on the internet have hacked the ROM and made their own versions of the game, some with stats changed, others with dialogue changes, and other stuff too. If there was such an alternate ending, I'm pretty sure such dialogue or other bits of code would have been discovered by now, much like how people have found out about monsters in the game that never appear, but still have stats, sprites, and even battle tactics present in the cartridge.

Shadow's not female. That's a rumour spawned from a translation error/problem in the English version if I remember rightly.

And as King Bahamut said, expanding on what you thought happened in this alternate ending of yours would be useful