Gatiss explained that the hour-long episode was only scrapped because the BBC chose to go with a 90-minute runtime.
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Speaking on BBC Four series Mark Lawson Talks To, Gatiss said that he and Steven Moffat chose to put the original recording on Sherlock's series one DVD to end the potentially damaging rumours.
"The pilot is very good," he said. "We would have been very happy [to air it]... We knew we couldn't just bolt on another half hour, so Steve rewrote it and we remade it with a different director.
"Because of an internal decision to make it in another format, this gossip got out. I remember thinking, 'If we don't show people that it wasn't a disaster, this will live with us forever'.
"The argument is that you preserve the final version, sacrosanct, but I thought that was an insult to the original director and the production. The second one is more stylish, but it's a different beast."
Mark Lawson Talks To Mark Gatiss airs on BBC Four tonight (April 3) at 10.50pm.
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