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Is there any mention of what happened to the Prometheus class warships as depicted in the Voyager episode "Message in a Bottle" and whether they were used in the Dominion War?

Based on the description and performance shown in the episode, those ships would be designed precisely for that type of conflict.

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Canon appearances

As @T.J.L. mentioned, the only canon appearances of the initially highly-classified Prometheus-type vessels were in:

Unfortunately, none of these involve battle during the Dominion War. However, the last instance is particularly interesting because it indicates that the Prometheus class survived canonically into the 26th Century and served in the most pivotal battle of the Time Wars, suggesting the overall success of the Prometheus design.

Extended universe

The Prometheus class has made several notable appearances in Star Trek's extended universe, including Star Trek Online ("Welcome to Earth Spacedock").

The appearances that are most relevant to the question are:

After the safe return of the Prometheus and the testing of the ship's multi-vector assault mode were completed, Starfleet had rushed the construction of two further vessels, the USS Cerberus and USS Heracles. Both of these vessels were in service by late 2375, and the Cerberus served as Admiral William Ross' flagship from 2376 to 2379. (From novels DS9: Avatar and TNG: A Time for War, A Time for Peace.)

(Source)

As the Dominion War ended in 2375, the timing above suggests that two Prometheus-class vessels may have seen action in the last few months of the war.

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    I haven't been able to justify buying one in STO. :) – T.J.L. Sep 1 '15 at 19:56
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    Although the Prometheus prototype had been built, the entire program was likely put on hold as Startfleet investigated the extent of the Romulan infiltration. As Message in a Bottle aired about half way through DS9 season 6, it's conceivable that it could have taken 18 months or longer for Starfleet to resume the project, thus barring the craft from participating in the Dominion War. That the Prometheus made an appearance when Voyager returned to Earth doesn't imply much. Anticipating a Borg attack, any nearby space-worthy vessel would have been used for defense, even a mothballed prototype. – Xantec Sep 2 '15 at 3:19
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    @Xantec : Those are fine speculations. Going on canon material alone, I would agree with you. – Praxis Sep 2 '15 at 3:21
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According to Memory Alpha, the only on-screen appearances were the feature episode, VOY 4x14: Message in a Bottle (used against Starfleet and Romulans), plus brief cameos in VOY 7x25: Endgame (versus Borg) and ENT 3x18: Azati Prime (against the Sphere Builders). None of the engagements feature Dominion forces.

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