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Putting this question into context.
A unit of Empire Swordsmen who have light armor and a shield, a 5+ armor save. They are unfortunate to have been affected by Plague of Rust so that would put their armor save at 6+. In the next turn they are even more unlucky and are affected by the same spell again. They now have no armor save.
If this unit were to go into close combat; after being affected by Plague of Rust twice, still have their 6+ ward save their shields provide them??
My reading of the rule is yes - their armour save is reduced every time the spell is cast on them but they still have the armour so they parry save from the shield should still be there.