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Well, it really depends on how much of the story the author has rough-drafted already. This happened with Toradora too, in that the anime was long done being broadcasted by the time the book series was finished. The result: the ending was slightly different.
The anime differed from the novels in relatively small ways until the last episode, which was quite different from the books.
Similarly, the Golden Time manga is different from the novels in tone, though not in the basic sequence of events. The main difference (to my mind) is that the manga makes Linda much more flirtatous than she is in the books.
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