Actually, no, you wasn'tI tried but I couldn't do it twice. Guess I was lucky one time. The key is to finish all of the fighters before depleting all heat sinks. An it's challenging to outmaneuver federal fighters.
Yes, once you work out the silent running mechanic it's basically a speed mission - you have to kill the fighters quickly. And sooner or later, heat sinks or no, the Cobra will spot you - the last fighter needs to be nearly dead by then. You need a solid handle on the combat mechanics, probably from replaying the earlier missions multiple times, to succeed at this one. It's not really a great showcase mission for stealth for this very reason - it's much more an advanced combat mission, as it's hard to conceive of any real situation you'd find yourself in where you want to ambush three ships while evading one you can't take out. You aren't going to get cargo from them since you can't afford detection, and I doubt most bounty or assassination missions will put you in a situation where you'll be kitted up to take out only the smaller targets.
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The trick is to make sure you stay away from the Cobra - aim at a fighter that it's close to, and it will find you immediately. Stay where you are, and you're in the direction it's coming and it will find you then too. You need to be pretty constantly on the move.
I haven't tried silent running in the main game yet, but in the scenario the Cobra is intended to find you (I've seen suggestions from more advanced pilots who can reliably get and stay behind it that the best option is just to do that and kill the Cobra, but I can't get on a ship's tail and stay there consistently). It may not work that way in the real game - just as, in the supercruise mission, if you drop without a destination lock you're sent back to your starting position, but in the real game you come out wherever you happen to be in space at that point.