Sometime before Stardate 54826.4 (October 29, 2377), the Tonawanda and the USS Danvers had been assimilated by the Borg Collective during their invasion of the Federation in that year. The Borg sent the pair of ships for deconstruction and analysis to Nexus NX-4288. Escorts consisting of Borg and other assimilated vessels accompanied the Tonawanda and Danvers and protected them from attacks by Species 8472. Both ships were deconstructed for study. (TNG video game: Armada II mission: "The Catch")
In the year 2385, the Tonawanda, under the command of Captain S'hirethal Verauk, was sent to the planet Jevalan in the Doltiri star system under direct order from then-President Pro Tem Ishan Anjar to apprehend Cardassian physician Ilona Daret and anyone in his company to prevent the truth of Ishan's true identity becoming public knowledge. The attempt to carry out this order resulted in a brief exchange of fire with the USS Enterprise-E and Captain Verauk being relieved of duty by her first officer, Commander Latanun. (ST - The Fall novel: Peaceable Kingdoms)
The Tonawanda's registry number is the same as that of the Nebula-class USS Prometheus. It is possible that the Prometheus was renamed sometime after the commissioning of the Prometheus-class starships.