The way I interpret it, the "C" always went to the future and then back again.
Than why do things change when it does come back?
Things change to how they were before Yesterdays Enterprise
Think of Doc Brown's chalk board in Back to the Future II
(sorry I am at work and cannot upload an image)...
Replace the 1958 in Doc Brown's chalkboard with the Battle of Narendra III (2344).
Replace Marty Mcfly's 1985 with the 2366 where the Federation and the Klingons are at war.
Replace the "hell valley" version of 1985 (the skewed future) with TNG depicted as the "primeline".