Deathwing is also present in the book Day of the Dragon. Most people thought he was dead, but he resurfaced and is defeated by the other Aspects, including Alexstrasza who was just rescued by a group of Alliance heroes. He eventually escapes.
The backstory in the Warcraft III manual, and the official Timeline published few months before the release of World of Warcraft, states that Beyond the Dark Portal takes place before Day of the Dragon. However, this actually creates lots of new problems.
Day of the Dragon describes the last war against the Horde, but the characters only speak about Orgrim Doomhammer and say he and the Horde were defeated "a few months ago". Yet Ner'zhul's forces actually began other wars a few months after Doomhammer's defeat, and no character speaks about it. On the other hand, Beyond the Dark Portal makes an open reference to "the liberation of the dragon queen Alextrasza". The Horde needed Deathwing precisely because the orcs needed other dragons to fight for them. According to both the book and the game, Day of the Dragon actually takes place before Beyond the Dark Portal.
One possible explanation is that Knaak wrote in his novel that the capture of the Dragonmaw clan was the end of the war against the Horde, which was correct, since Doomhammer and Ner'zhul's forces were two distinct groups. People that wrote the timeline may have incorrectly thought it happened after all the wars between humans and orcs. None of this has ever been confirmed or denied.