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According to the Daily Star, filming for the special "has been thrown into jeopardy" by the loss.
Executive producer and lead writer Steven Moffat is said to be "facing a race against time to create a new draft before filming commences next month".
Moffat also allegedly revealed that the episode would be "a flashback Christmas special."
The final episode of the programme's fifth series aired on June 26. A new series is expected to follow the Christmas special in 2011.
It was previously revealed that past Who writers Paul Cornell and Tom MacRae may be returning for the show's sixth series.
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