Been years since I made that mission but as I remember there is a random failure you sub will get- damage, flooding etc and your mission orders are randomized.
Not sure how you were counter detected. Maybe the FF in the mission got you in a CZ. This mission was made a long time ago and may not be adjusted for the latest LWAMI mod.
Were you using LWAMI or stock? or some other mod. If you were using LWAMI the only thing I think might have happened was the PTG got a visual on you if you were at PD.
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