i know the problem well, i too spotted that carrier in lock ewe, got lucky and managed to sink it with 4x impact detonations, it wont sink unless you get the critical shot, if you dont, it will sink by flooding and when it bottoms out it`ll sink no further, the chance of this critical hit is lessened with 100% difficulty and mods like nygm/gw.
i dont know of anything you could do to fix this unless you lower the realism settings which isnt really an option.
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