They're essentially in name only as their character are different too.
Well, I doubt that problem would happen with Fang, since his personality is such a large part of his character!
A pet peeve of mine is when Sonic's transformations (Super Sonic, Darkspine Sonic, Werehog, whatever) are treated like completely different characters.
I hate this too. Although to be fair, Super was a separate entity in Fleetway (and Sonic Shuffle), so I can understand how people might make that mistake.
Charmy really didn't have much of a character description in Chaotix, he had plenty in that manga he first appeared in but game wise not much before Heroes, so saying they changed his character is kinda debatable.
The only thing we really learned about Charmy in KC is that he loves flowers, which was retained (and expanded on) in Heroes.