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A question that came up in a friendly game the other day, what happens when an instant death cc weapon is used on a vehichle?

Nothing. Instant Death CC weapons don't have anything special against vehicles. (Unless they have rules for damaging vehicles as well.)

That clears that up.

The vehicle loses all remaining wounds if it fails its save.

Oh wait, vehicles don't have wounds.

ID is a rule that effects units/models with a wound profile.
Vehicles do not have one, so are unaffected.