I think the only time an entity warps away and returns to full health is when it gets too far from its spawn point.
To kill the device is easy if you are patient and play to the limitations of the BoP. The BoP will die if it gets shot by pretty much anything, so staying near the device is lethal as the klingons will kill you if the Device doesnt. Just fly circles around it at 10.1 km and as soon as it fires at you, move forward and shoot the missile then retreat again. Do this a few times and the device is dead. You can shoot it for I think it was 3 seconds after it has fired, any other time it is invulnerable.
To facilitate this tactic, use the max power to engines setting for increased speed/maneuverability to get you in and out as quickly as possible. (Since your disruptors won't work against the Device, weapon power doesn't matter.) Evasive Maneuvers also helps you get out of the firing cone or blast radius after you make your torpedo run.