Come on guys, this is obvious. Shapeshifter Charlie went forward in time to film this episode and then went back with the knowledge that he had been written out. He tried to stop this, but JJ said no and said he could come back as real Charlie when they had filmed the resurrection episode in series 3 (where Charlie, John and original Bell are brought back from the dead). Hence, the Charlie we will see is still the dead Shapeshifter, although in series 3 it will be revealed that it is original Charlie, who went back in time to prevent...ahh, but that would be telling.
Wow, these mushrooms are strong.