Rumours circulating that Canadian developer Silicon Knights was facing job cuts due to a financial falling out with Nintendo, appear to have been unfounded.
President Denis Dyack confirmed that the studio behind Eternal Darkness had indeed been forced to lay off a number of employees, but shot down speculation that the job cuts were caused by Nintendo pulling funding for a rumoured Eternal Darkness 2, following a ruling against the studio in a lawsuit against Epic Games. Silicon Knights was ordered to pay $4.5 million in damages to Epic Games in that case, which would seem to be the main cause for the current job cuts.
…it is not true and has no basis in fact.
~Denis Dyack on Nintendo rumours
Nothing regarding Eternal Darkness 2 (such as whether or not it exists) has been revealed.