There is a book called "Ship of the Line", which explains the events you are looking for. It describes how the Bozeman helped to stop a Klingon invasion force that was hiding in the expanse, which was still on the Klingon side at the time. The Bozeman herself, was a border cutting vessel, much like that of the United States Coast Guard.
A diversionary tactic was used by the Klingons to panic a task force into thinking a Klingon fleet was massing somewhere else, when in reality they were in the expanse. Since Kozara, the leader of the Klingon Fleet, had a personal vendetta against Bateson and the Bozeman, he made it a point of honor to detroy the Bozeman before it could warn the fleet. According to the Kozara's XO, both ships were still at least 3 hours from Starbase 12 at Warp 5. Communications were blanketed by the Klingons and the attack began.
The Bozeman, heavily damaged made a run for it and found a system to hide in, which also gave them time to launch a "hardshell" beacon, set to go off 30 minutes after launch, giving it time to get far enough away from the Klingons and to warn to fleet of where the Klingons were actually staging. The Bozeman found an area of space that was described as a "hazy globular mass" which gave them a good place to hide. This was the phenomenon the Enterprise-D came across and encountered the Bozeman.
The ploy worked. The beacon sent the message to the fleet and Starfleet was able to stop the Klingons, but there was no sign of the Bozeman. Because the expanse was still on the Klingon side, it's most likely that starfleet labeled the ship as missing. It's also likely that since Kozara presumed the ship was destroyed, that he didn't bother with trying to find too hard where they went when they realized back up was on the way. Chances are that the message sent was short and to the point, and since in the book the crew of the Bozeman figured this would be a suicide mission, they figured what was most important was getting the message about the Klingons out, and less about themselves.