Yeah, that's probably something you're just going to have to just keep wondering.
Exactly. It's possible that there was a way to write Clone Conspiracy and Ben's character in a way that was familiar, whilst still bearing the scars of what happened to him. But that's not the story Dan wrote. And it certainly wasn't the Ben that he wrote. CC's Ben didn't even have a mild echo of Ben's personality, not a single line of dialogue, not a single action, not a single solitary moment that felt in any way at all like this was a damaged Ben Reilly.
Indeed, take out some of the personal stuff and you could have given any generic villain exactly the same dialogue that Ben had in this story and I doubt anyone would have suggested "Hang on, that sounds like something Ben Reilly would do/say".