Welcome to the secret special stage

A while ago, I mentioned how there's this obscure feature of debug mode wherein if you hold down the A button while a special stage is loading, which stage is actually chosen is determined by the value of the Sound Test option rather than which emeralds have been collected. This wraps around every eight values, so $00 and $08 both yield stage 1, etc.

For this reason, whenever the Sound Test value ends in either a 7 or an F, the player is taken to a secret special stage, stage 8. Curiously, despite the fact that this stage is never seen during normal gameplay, its palette is actually different between Sonic 3 (left) and Sonic & Knuckles (right):

If you manage to clear this excruciatingly long stage, you're rewarded with the nonexistent eighth chaos emerald, which shares its color with the Flying Battery Zone-themed stage 5:

However, when you clear the same stage in Sonic & Knuckles, the emerald you're awarded is yellow instead:

This is interesting because in Sonic 3, the yellow emerald is the one obtained in the Hydrocity Zone-themed stage 2! In Sonic & Knuckles, it was changed so that stage 2's emerald is orange instead:

So what is the reason for this whole switcheroo? Well, it turns out, the super emeralds from Sonic & Knuckles reuse the same set of palettes as the regular emeralds.

What probably happened is the yellow super emerald was made orange in order to match its sprite from Hidden Palace Zone, and this change retroactively affected the color of the regular emerald as well. Then, since it didn't have a unique color of its own, the eighth emerald was given the (now unused) yellow palette.