Light spoilers below! TL;DR after the paragraphs.
This comes from the VOY episode "Message in a Bottle" (4x14, really good imo.)
The Doctor travels through Hirogen relay stations to a Starfleet ship in the Alpha Quadrant. The ship is the USS Prometheus, a prototype ship designed for deep space tactical missions. It had a unique ability called the multi-vector assault mode, where the ship could break apart into three warp-capable vessels. The saucer section deployed its own warp nacelles, and it looked strikingly similar to the USS Protostar of Prodigy. Another similarity between the Prometheus and the Protostar is that there is holographic imaging systems on all decks. Oh, and the Prometheus was the fastest ship in Starfleet, as it was able to reach warp 9.99. The proto-drive of the Protostar makes it the fastest Starfleet ship of its time too.
This led me to the idea that maybe the ship Dal & everyone else found in Prodigy could be only one part of a whole vessel. It seems that the Protostar is modeled after the Prometheus, since the holographic systems, purpose, and warp capabilities are similar. If you care to compare the look of the two ships, the Prometheus wiki has an image of the saucer section after multi-vector assault mode is enabled.
There's no way to know what the Diviner meant when he said Chakotay was taken prisoner (likely not by him, since he could've found the Protostar immediately). But maybe Chakotay and some of the crew of the Protostar are on different sections of the whole ship?
TL;DR - The USS Prometheus from VOY shares similar technology with the USS Protostar of PRO. They both are the fastest in Starfleet at the time, they both have holographic systems on all decks, and their missions are similar. It could be possible that the ships also share the ability to enter multi-vector assault mode, where they break into separate warp-capable vessels. This means Chakotay and part of his crew could be making their way in the Delta Quadrant on parts of the whole Protostar.
