Yep.
Best thing to do is pretend whatever was brought back in Clone Conspiracy wasn't the real Ben at all. And given that story's completely ludicrous explanation for his existence and behaviour, isn't a huge stretch.
As far as I'm concerned, if Marvel ever really wanna bring Ben back properly, I'd just retcon the end of Revelations so that the Ben who sacrificed himself was another clone that Norman created (cos let's be honest, he was churning those things out like a factory), whilst still keeping the real Ben prisoner. Ben subsequently escaped, realised he was 'dead' again and after discovering that he really was the clone, he came to terms with it, because he realises he doesn't feel any different to when he thought he was the real Pete.
Deciding that staying in New York and revealing himself to Pete again would only complicate matters and likely put them and their friends/family in more danger again, Ben decides to once again hit the road. Only this time, not as a reluctant hero and recluse, but now actively seeking out people that need his help. Basically 'The Lost Years', but with a more positive, pro-active (but still sans-costume) Ben... Still the hero that he always was.
All of which means we can rightfully consider the events of Clone Conspiracy and the subsequent Scarlet Comic to be the adventures of a completely different character who had nothing in common with Ben whatsoever. Which is extremely easy to do, because that's exactly how it was written.