I do remember there being very real doubt at the end of Season 3 whether CC would be back at all in Season 4.

That said, I cannot pretend to have liked Whedon's plot of possessed Cordy in Season 4. In fact, I rather hated it. It's one thing to have issues with an actress, but sheesh, don't destroy your own characters in a fairly un entertaining way. I don't know much of anything about CC and whatever were her issues, but the character of Cordy didn't deserve that.