100% repeatable? That sucks.
I guess my question is why is there a link being created in the first place on that particular mission. Those convoy ships have little navigational radars that are useless in this fight, and if memory serves me correctly the embarked helos aren't on alert status.
If the helo is airborne, it might change things to delay its takeoff a bit so that it can't link anything. Maybe try toggling REMRO if it is airborne too, or for that matter toggling surface search or maybe even Show Allies. These are all just guesses, I don't understand the bug enough to predict its behavior.
And yes, chaff can still get the job done as long as the chaff is inside the acquisition cone of the missile, so it helps if you're between the missile and the intended target. Maximum acquisition range is 80km (43nmi) so have the chaff out before it gets that close.
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