There was no mention of Great Moments with Mr. Lincoln being added to the new Walt Disney Story being created for DCA. This show is indeed different than the one that was shoehorned into Great Moments with Mr Lincoln, as it is placed as the pre-show before the Lincoln presentation. I imagine there will be some alterations to the pre-show when Mr Lincoln returns, however since the approach is very different than the DCA show I can still see it staying in the Opera House before Lincoln.
But seeing as Walt Disney and California will be the new focus for The Walt Disney Story being created for DCA, I don't see any room for Lincoln in the mix. I think it's safe to say there will be no Lincoln as part of this show.