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So, seeing as I didn't even start Green until I was done with the third badge, and the fact that it wasn't the right Green version (aka Japanese Blue), but instead just a copy paste of Blue, I have decided to restart the runs.
I also added one more rule, not only is dupe clause implemented across all four runs, but also across gens. So if I catch say a Pidgey in Yellow, I can never catch another one in GSC or FRLG games, even if it faints.
This is the ultimate autism test.