How were they able to re-emerge united by Nurhaci centuries later? Were they simply allowed by the Mongols under Genghis Khan to move back to their homeland in what is now modern day Manchuria? Or maybe a portion of them had always stayed behind in Manchuria and didn't settle down in Northern China?
Many of the Jurchen whom still inhabited Manchuria around the time of the Mongol conquest of Jin (1228) were not sinicised, unlike those of the Jin ruling caste. These peoples would come to constitute part of what the later Ming would describe as the "Wild Jurchen", the northernmost Jurchen/Manchu whom still observed traditional customs and not influenced by Chinese ideas such as Confucianism - unlike the Jianzhou and Haixi Jurchens to the south, the resultant power struggle between which leading to the ultimate conquest of China and the establishment of the Qing dynasty.
In fact the first Mongol invasion of the Jurchen Jin - where submission was the clear goal rather than outright conquest - resulted in the seizure of Beijing in 1215, at which point many steppe peoples [Jurchen and Khitan] within the Jin's ranks defected to the Mongol side.
By the time of the Mongol conquest of Jin in 1228, almost none of those remaining were Jurchen, with the state now essentially run, fought for and represented by Han Chinese. Subsequently the vast majority of Jurchen peoples either continued to assist the Mongols in their invasion of China or submitted and returned to the steppe, be it parts of Mongolia or Manchuria. The goalposts of Mongol invasion shifted dramatically; by now the total submission of China was the goal, and the Jurchens were effectively assimilated into the Mongol state either as part of the war machine or as a native populace which migrated back to the North East [Manchuria].
Interestingly it is this turn of events which lead to the reinvention of the Jurchen as Manchu - the connotations of Jin were seen as undesirable and a new identity for a new dynasty was forged. It is also important to note that the Qing conquest of China was not a Jurchen/Manchu achievement alone. Many of those who entered Beijing in 1644 to conquer were Mongol - by now denoting a much more varied ethnic group than before including those descended from Turkic and Khitan peoples - not exclusively Manchu/Jurchen. These peoples saw more in common as inhabitants of the steppe than the Han which were seen as very much distinct.
Source: China: A History - John Keay