So apparently, after activating a bad end, you are expected to go back to the base, use the Control Panel to put out the Hourglass you received during the bad ending, and use that to "Time Travel" in order to remove permalocked equipment? Is that right?
That essentially is a New Game +, as it resets your money, keys, and crystals to 0, removes any Deadkeys/Deadkey pieces from your inventory/wardrobe, and resets your current equipment to the Control Suit, whether you were wearing it at the time or not. You keep anything else in your wardrobe that wasn't a Deadkey or Deadkey piece, and you keep the furniture you had in the Control Panel (minus the Hourglass).