I know this thread is a couple of years old but I'm playing the Pokemon Spirit Emerald hack rn on this website link:
https://www.playpokemongames.net/spirit-emerald-432.html
I ran into the same shiny stone glitch, as well as some of the others (ie. the respawning egg givers). I've saved my state as a file, but play the game via the website and uploading my saved file. I couldn't tell by this thread, but was there ever a way that was determined to successfully avoid the shiny stone glitch... while also keeping my current game data? I'm only asking because I really enjoy this hacked ROM and am hoping to access the items I have received after the shiny stone. Thank you