Siliconera noted, the new trademark differs from the 2010 renewal due to the addition of coverage for "downloadable electronic game programs; downloadable electronic game software."
At face value, the change in language for the Eternal Darkness trademark could simply be the lawyers covering their bases. That's what they're paid to do. Especially when there's the potential need to enforce it with Shadow of the Eternals.
Then again, sometimes these trademark renewals are the sign of something legit, as was the case with Killer Instinct. A digital release of Eternal Darkness on the Nintendo Virtual Console is an option available to the publisher.