If it turns out he didn't have in his system what he tested positive for, also if they don't have a clause written in that protects even if that is the case (which I HIGHLY doubt), then yes. In all reality though, they probably have a clause written to protect them, he also probably did test positive for what they say he did.
We all know what's happening here, his team have gone out and found a supplement that had the substances he tested positive in them but aren't disclosed on the label, they'll just tell USADA he took that. I'm sure you can go over to the Bodybulding.com Forum and ask for a bunch of supplements at GNC that have real anabolics or anti-estrogen substances in them. I don't know how far down the rabbit hole USADA will go, if they'll ask him questions like where he bought them from? Where's the proof he bought them? How did he take the supplement? What does it taste like? Etc. Even if they do, when we're talking about a 2 year ban over a 6 month ban which could cost Jones' and his team $10 Million, they'll probably have their bases covered.