Not really an issue, the word 'dismantled' is highly ambiguous.
This was already established by the Word of Blake's Farragut. Artwork of the Farragut in Liberation of Terra doesn't establish the Farragut's service during the Amaris War, or its presence in the Exodus fleet, however.
Alternate theories:
1) The final Farragut was rendered fully non-operational by december 20th by removal of critical systems, but the majority of the hulk remained intact for later disposal. The most important element of a combat warship, and the hardest to remove, is the KF drive. The Amaris Coup interrupted the final scrapping and recycling of the hulk, leaving an intact drive core and superstructure, unsuitable for restoration in the short term, but ideal for long term restoration by the Word of Blake. This is in line with Star League practices that tended to just leave "scuttled" but restorable warship hulls just laying around.
2) The Word of Blake Farragut is in fact new built, possibly at one of the five worlds. It is established that Comstar had an active warship construction program until the mid 30th century. It's also established that the Comstar we know only scratched the surface of what they were up to before the schism. Much like the five worlds themselves, the Farragut could have been something that the official Comstar didn't know about, and was only activated once the Master took a more active role in the Word of Blake. I actually consider this explanation less likely, as there are battleships more suited to the needs of old school Comstar than the Farragut.
3) More whimsically, the Word of Blake Farragut was a derelict left over from the Reunification War. The war on the Taurian Front was a bloody affair, and until the battle of Robsart the Taurian navy was consistently giving as good as it got. It is possible that Concordat forces at some point took out a Farragut, enough to force the ship's abandonment, but not enough to completely destroy it, and the location of the wreck was lost until being rediscovered much later. If I were going to spin it into a story, I'd pick the Pleiades campaign as the point where the ship was lost, and have it rediscovered by Word of Blake advisors following the Taurians when they invaded the cluster during the 3060s. I have no evidence for this theory, but it makes me smile.