Corrected entry: In other episodes once the doctor has been deactivated outside sickbay his mobile emitter falls to the ground and we see it. In this episode in engineering when the doctor is deactivated we don't see the emitter.
Corrected entry: In engineering just before the doctor was deactivated he said "I tied" twice.
Correction: The ships systems are being affected by the nebula they're flying through, this could be a effect of this.
Correction: In "The Killing Game" Hirogen & some Starfleet crewmembers install holo-emitters thoughout most of the ship, including corridors, the mess hall, astrometrics & engineering (we know this as one of the Hirogen hunters brings a rifle into engineering). The holo-emitters should still be working.
There is no evidence that what the Hirogen did to Voyager was retained. We can only assume that Voyager's reset button returned the ship to factory settings after "The Killing Game." Indeed, the Doctor always wore his mobile emitter when in engineering throughout the rest of the show.