Probably just one sect/ship that found the Borg transwarp post-“Endgame”, ventured out and became mercenaries.
Asencia says decades passed. So the timeline is approximately:
2381 or 82 - The Protostar is launched. After a time, it passes through a temporal anomaly and dissappears.
2383 - Dal and Rok find the empty Protostar buried in Tars Lamora and fly it out with the other Prodigies. After no responses from Chakotay to Starfleet Command, Admiral Janeway mans a rescue mission to track down Chakotay once a few protojumps are detected (done by our crew.)
2384 or 85 - A Federation ship, seemingly Prometheus class, makes first contact with Solum. Civil War erupts, and The Federation can’t intervene due to the Prime Directive. This is further complicated after the attack on Mars and Starfleet policy changes to be more isolationist due to loss of thousands of ships.
2385-2430(?) - After decades of civil warfare, a wormhole “tears open the sky” and the Protostar emerges. Chakotay and crew are captured. The Protostar is refitted into a Trojan horse ship with plans to send it back through the temporal wormhole over Solum. Chakotay and some of the remaining crew stage a prison break and, unable to board the ship, activate the launch sequence without a crew so it flies through the unstable time wormhole and is lost in the past. The other Vau N’akat also try to follow, but it collapses mid journey and only a few survived, landing in random points throughout history.